Name: A unique identifier for this aligned sequence
Type: The type of alignment, in this case “match”
Score: Mapping Quality score. This score equals -10 log10 Probability{mapping position is wrong}, i.e. minus 10 times the log base 10 of the probability that the mapping position is wrong.
Position: The genomic position where the sequence read hits on the genomic sequence, going from the first base that aligns to the last base that aligns, including the length of any unaligned segments that are enclosed in the alignment. In this case, the position is ” Chr5:168613773..168613961 (+)”. The alignment includes a segment from 168,613,773 to 168,613,857 indicated by a light red block and another segment that aligns from 168,613,945 to 168,613,961 (the light red block to the right), with a segment of the reference from 168,613,858 to 168,613,944 where the RNA sequence does not align, as indicated by the black line between the blocks. The strand of the genomic reference sequence to which the RNA sequence aligns is indicated by a “(+)” for forward, as in this case, or “(-)” for reverse.
Sequence and Quality: The nucleotide present at each position of the alignment displayed above the quality score for that single nucleotide alignment. The base quality score is -10 log10 Probability{base is wrong}, i.e. minus 10 times the log base 10 of the probability that the base given is wrong. These same quality scores and nucleotide sequence are also listed separately toward the bottom of the popup.
AS: Alignment score generated by the aligner. A “0” value means the information is not available.
CIGAR: A “string” of letters and numbers giving information about how many nucleotides on the reference sequence that were Matched (M) or Not Matched (N, indicating a skipped sequence from the reference) by nucleotides in that “read” of the sequenced RNA, counted from the alignment’s start position to the stop position and shown in order from left to right. In the example here, the CIGAR “string” is 85M88N16M, i.e. beginning at Chr5, base pair position 168,613,773, the alignment consists of 85 nucleotides on the reference sequence which Match, 88 nucleotides on the reference sequence that are Not matched and 16 nucleotides on the reference sequence which Match, ending at base pair position 168,613,961. Additional options are available. See the SAM file format for the complete list.
MD: A string for the mismatched positions in the aligned sequence. If all positions match this will be the number of aligned nucleotides (i.e. the length of the aligned sequence).
MQ: Mapping Quality score. It equals -10 log10 Probability{mapping position is wrong}, i.e. minus 10 times the log base 10 of the probability that the mapping position is wrong.
NH: Number of reported alignments that contains the query in the current record. “1” indicates that the RNA sequence only aligned once to the reference.
NM: Edit distance to the reference, including ambiguous bases but excluding clipping
XG, XM, XN, XO, XS, YT: These are “user defined” tags. In general, a “0” value means the information is not available.
Duplicate: Indicates whether or not this read alignment a duplicate of one or more others.
Length on ref: The length of the reference genome sequence covered by the alignment, including the matched sequences and the segment(s) on the reference that were skipped.
Multi segment all aligned: If the RNA sequence aligned in multiple segments, were all of those segments successfully aligned to the reference?
Multi segment first: If the RNA sequence aligned in multiple segments, is this the first of those segments?
Multi segment last: If the RNA sequence aligned in multiple segments, is this the last of those segments?
Multi segment next segment reversed: If the RNA sequence aligned in multiple segments, does the next segment in the alignment match the opposite strand relative to this one, i.e. if this segment aligns to the forward strand, does the next align to the reverse strand or vice versa?
Multi segment next segment unmapped: If the RNA sequence aligned in multiple segments, was the next segment not able to be aligned to the reference sequence?
Multi segment template: Did the RNA sequence that this refers to (i.e. the one contiguous chunk of sequence that came off the sequencing machine) align to the reference in more than one segment?
Next segment position: If the RNA sequence aligned in multiple segments, what is the genomic position of the first nucleotide in the matched sequence of the next segment?
Qc failed: Did this alignment pass or fail quality control?
Qual: The single nucleotide quality score for each base in the alignment. These are the same scores listed above with the sequence.
Secondary alignment: Is this a secondary alignment?
Seq: The RNA sequence that was aligned. This is the same sequence listed above with the corresponding single nucleotide quality scores.
Seq length: The length in nucleotides of the aligned sequence.
Seq reverse complemented: Is the sequence listed above reverse complemented relative to the reference sequence?
Source: The name of the BAM file from which the data was derived.
Supplementary alignment: Is this a supplementary alignment (see the information above regarding the context-specific menu parameter for “Hide supplementary alignments”).
Unmapped: Is this alignment not mapped to the reference assembly? |