BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525220.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 = 1,319,503 number of mapped reads = 1,183,641 (89.7%) number of supplementary alignments = 3,271 (0.25%) number of secondary alignments = 0 number of mapped bases = 68,279,846 bp number of sequenced bases = 68,258,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,530 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5467 >>>>>>> ACTG content number of A's = 17,295,353 bp (25.34%) number of C's = 12,524,085 bp (18.35%) number of T's = 22,058,508 bp (32.32%) number of G's = 16,378,985 bp (24%) number of N's = 1,511 bp (0%) GC percentage = 42.34% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 355,109 number of insertions = 4,726 mapped reads with insertion percentage = 0.4% number of deletions = 13,453 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.11% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.2341X There is a 2.03% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 7203245 0.028899607034479566 0.40348711179316554 chr2 243199373 6011920 0.024720129521057607 0.3228225439537399 chr3 198022430 5245351 0.02648867100560275 0.1766536366198165 chr4 191154276 3742722 0.019579588164692692 0.15608755103846025 chr5 180915260 3023366 0.01671150349616721 0.13804475453012538 chr6 171115067 4232195 0.024733035343988734 0.18594600345387552 chr7 159138663 4996901 0.03139966684274581 0.3979840783561119 chr8 146364022 3876724 0.026486864374361072 0.21586369429585678 chr9 141213431 2229679 0.01578942586558923 0.17234497780393399 chr10 135534747 3675181 0.0271161534687485 0.26643090244389506 chr11 135006516 3603595 0.02669200796204533 0.19652566936230353 chr12 133851895 2843957 0.021247043233866805 0.15694511751862975 chr13 115169878 2100310 0.018236626073355744 0.14629798079348352 chr14 107349540 1951587 0.018179742549432443 0.14850060649419577 chr15 102531392 1880833 0.01834397215635188 0.14710600531205528 chr16 90354753 1956908 0.021658052675989276 0.17123500534915168 chr17 81195210 1279977 0.015764193478901033 0.1376668825735833 chr18 78077248 1433583 0.01836108516529681 0.2679206409429397 chr19 59128983 1214284 0.02053618950287036 0.27897109751442656 chr20 63025520 1398151 0.022183886781100736 0.16144512927079485 chr21 48129895 868495 0.018044813935289075 0.15100780113199658 chr22 51304566 553326 0.010785121932422155 0.11080089124300796 chrMT 16571 5552 0.3350431476676121 0.6339537185394372 chrX 155270560 2760424 0.017778154467917164 0.15471751466373945 chrY 59373566 191580 0.0032266884559367715 0.09961390915871593