BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6237293.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 2,801,386
number of mapped reads = 2,465,468 (88.01%)
number of supplementary alignments = 16,609 (0.59%)
number of secondary alignments = 0
number of mapped bases = 163,797,224 bp
number of sequenced bases = 163,728,228 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 144,321
duplication rate = 4.34%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8153
>>>>>>> ACTG content
number of A's = 45,512,206 bp (27.8%)
number of C's = 29,608,968 bp (18.08%)
number of T's = 52,484,527 bp (32.06%)
number of G's = 36,119,951 bp (22.06%)
number of N's = 2,576 bp (0%)
GC percentage = 40.15%
>>>>>>> Mismatches and indels
general error rate = 0.0081
number of mismatches = 1,306,691
number of insertions = 13,108
mapped reads with insertion percentage = 0.53%
number of deletions = 39,640
mapped reads with deletion percentage = 1.59%
homopolymer indels = 47.56%
>>>>>>> Coverage
mean coverageData = 0.0529X
std coverageData = 0.5329X
There is a 4.22% of reference with a coverageData >= 1X
There is a 0.74% of reference with a coverageData >= 2X
There is a 0.15% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 18480627 0.07414475809871704 0.8398375699866308
chr2 243199373 12417312 0.05105815795010294 0.5974564262061093
chr3 198022430 9162988 0.04627247529484412 0.2559976166006379
chr4 191154276 8229940 0.04305391525743322 0.35270619484302246
chr5 180915260 9690295 0.05356261821142119 0.284919530453018
chr6 171115067 15255835 0.08915541610371458 0.4925141605187169
chr7 159138663 9409885 0.05913009964146802 0.7963498870549777
chr8 146364022 9328063 0.06373193953361024 1.0337610597330698
chr9 141213431 8404905 0.05951916145993223 0.5570885438762715
chr10 135534747 7006462 0.05169495022556835 0.5045104406234109
chr11 135006516 4762785 0.03527818612843842 0.3195654420447477
chr12 133851895 4909505 0.03667863648848602 0.2533396732440061
chr13 115169878 6993949 0.06072724154487687 0.29685704637177684
chr14 107349540 5320734 0.049564571958109926 0.30386121027782914
chr15 102531392 5012960 0.048891953012790465 0.27747033822391465
chr16 90354753 3073017 0.034010573854371555 0.27669509173781304
chr17 81195210 4458380 0.05490939674889689 0.342353390377953
chr18 78077248 4951429 0.0634170533264697 0.9642866675282211
chr19 59128983 2552852 0.043174292377056445 0.5362118365113269
chr20 63025520 3337480 0.05295442227212088 0.29121936259607495
chr21 48129895 2241548 0.0465728836516265 0.3299158405235655
chr22 51304566 1220722 0.02379363271487376 0.1785093408327026
chrMT 16571 53237 3.212660672258765 3.0661583378319834
chrX 155270560 7077198 0.04557978022363029 0.30387176780397657
chrY 59373566 445116 0.007496871587601796 0.2559232204779785