BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716218.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 = 1,764,694 number of mapped reads = 1,593,883 (90.32%) number of supplementary alignments = 9,482 (0.54%) number of secondary alignments = 0 number of mapped bases = 92,958,230 bp number of sequenced bases = 92,931,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,606 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4898 >>>>>>> ACTG content number of A's = 22,929,882 bp (24.67%) number of C's = 19,406,530 bp (20.88%) number of T's = 29,244,521 bp (31.47%) number of G's = 21,349,303 bp (22.97%) number of N's = 1,133 bp (0%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 457,253 number of insertions = 7,716 mapped reads with insertion percentage = 0.48% number of deletions = 17,034 mapped reads with deletion percentage = 1.06% homopolymer indels = 39.78% >>>>>>> Coverage mean coverageData = 0.03X std coverageData = 0.2842X There is a 2.65% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7751614 0.031099677781745626 0.3822971206965196 chr2 243199373 9234882 0.03797247454252277 0.3781758441393063 chr3 198022430 6870067 0.03469337791683497 0.21786029612976515 chr4 191154276 5173390 0.027063951213939886 0.20769230275365447 chr5 180915260 4663505 0.02577728932318921 0.17800434950736466 chr6 171115067 5135954 0.030014621681444333 0.20829457263529982 chr7 159138663 5209554 0.03273594173654708 0.5496501335369126 chr8 146364022 6637478 0.045349109086384634 0.31931516616965944 chr9 141213431 3921898 0.02777283982286359 0.2123926699685145 chr10 135534747 4466489 0.032954567731623835 0.3842934663331798 chr11 135006516 2767354 0.020497929151804792 0.19657648902894628 chr12 133851895 4361208 0.03258234035461358 0.2186738222678105 chr13 115169878 2400954 0.020847065584284112 0.15987757404448003 chr14 107349540 2963844 0.027609284585662874 0.18546997804395637 chr15 102531392 2241252 0.02185917850408195 0.16382232807770708 chr16 90354753 2887235 0.03195443409601264 0.20642403397505435 chr17 81195210 4011726 0.04940840722008109 0.25777199521656846 chr18 78077248 2151946 0.027561755250389973 0.33088981424013003 chr19 59128983 1977198 0.03343872834748401 0.3502632399385959 chr20 63025520 2145692 0.03404481232364287 0.21355271531258846 chr21 48129895 969590 0.020145275613005182 0.1784390983980113 chr22 51304566 1487091 0.028985548771623952 0.18816036912679365 chrMT 16571 45334 2.7357431657715288 2.290238231985469 chrX 155270560 3254287 0.020958815373629102 0.18098921901097667 chrY 59373566 228688 0.003851680392584134 0.11697259089118435