BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716649.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,213,545 number of mapped reads = 2,010,684 (90.84%) number of supplementary alignments = 59,358 (2.68%) number of secondary alignments = 0 number of mapped bases = 152,188,100 bp number of sequenced bases = 152,130,112 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,328 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0724 >>>>>>> ACTG content number of A's = 39,058,278 bp (25.67%) number of C's = 31,897,450 bp (20.97%) number of T's = 44,983,415 bp (29.57%) number of G's = 36,172,620 bp (23.78%) number of N's = 18,349 bp (0.01%) GC percentage = 44.74% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,181,732 number of insertions = 12,977 mapped reads with insertion percentage = 0.64% number of deletions = 33,008 mapped reads with deletion percentage = 1.62% homopolymer indels = 40.09% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.3635X There is a 4.26% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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% 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 12641602 0.050718437327383833 0.5746621484263492 chr2 243199373 14308073 0.058832688684604464 0.4853589541315968 chr3 198022430 11077896 0.05594263235735467 0.2724955303464087 chr4 191154276 6095687 0.031888834126838995 0.2166256153241855 chr5 180915260 9340736 0.05163044842099002 0.25724776182615416 chr6 171115067 11364287 0.06641312889180004 0.32714935425289343 chr7 159138663 7940327 0.049895649808243014 0.5090917261002386 chr8 146364022 9722024 0.06642359144790377 0.3949298281677496 chr9 141213431 6898385 0.048850771142300194 0.30852584687319684 chr10 135534747 7074989 0.05220055488796537 0.3644761784171105 chr11 135006516 6507202 0.04819916988302994 0.30743304075665684 chr12 133851895 5149389 0.03847079639776486 0.21921642404036984 chr13 115169878 5198569 0.04513826957427184 0.237449178923315 chr14 107349540 3765366 0.03507575346852907 0.2289489994165491 chr15 102531392 3695317 0.03604083518148276 0.21280227639406707 chr16 90354753 4672394 0.05171165705029375 0.2827490410492318 chr17 81195210 5541939 0.06825450663900001 0.31997858933728035 chr18 78077248 3286118 0.0420880356848643 0.6288760896671357 chr19 59128983 3347712 0.056617107721944074 0.4700982201955514 chr20 63025520 3395552 0.05387582680793431 0.28595370254494623 chr21 48129895 3287336 0.06830133329815076 0.30671192600889735 chr22 51304566 2976122 0.05800891094176686 0.2809328493537484 chrMT 16571 85519 5.160762778347716 4.136425601112957 chrX 155270560 4486247 0.028893094737341064 0.22279490625455414 chrY 59373566 329312 0.00554644132373656 0.17783082833120067