BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717085.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 = 2,072,377 number of mapped reads = 1,877,843 (90.61%) number of supplementary alignments = 29,817 (1.44%) number of secondary alignments = 0 number of mapped bases = 147,740,902 bp number of sequenced bases = 147,678,487 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,227 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0769 >>>>>>> ACTG content number of A's = 38,527,923 bp (26.09%) number of C's = 27,161,613 bp (18.39%) number of T's = 45,749,656 bp (30.98%) number of G's = 36,230,754 bp (24.53%) number of N's = 8,541 bp (0.01%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,234,306 number of insertions = 15,065 mapped reads with insertion percentage = 0.79% number of deletions = 35,565 mapped reads with deletion percentage = 1.86% homopolymer indels = 43.03% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.5163X There is a 4.03% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 11745812 0.047124504456099225 0.8253821743722904 chr2 243199373 13575199 0.055819218744449645 0.7482562379155103 chr3 198022430 9925413 0.05012267044697916 0.25999045882558464 chr4 191154276 9393344 0.049140119680085 0.28216519999292555 chr5 180915260 8566934 0.04735329678657289 0.2547255315419004 chr6 171115067 8724098 0.050983809625601235 0.3373543727074018 chr7 159138663 8206137 0.05156595415156906 0.6598410421885847 chr8 146364022 7725967 0.0527859708583302 0.6906299617085446 chr9 141213431 6133230 0.043432341786242695 0.6010645322446254 chr10 135534747 6877752 0.05074530444949294 0.5219970479754378 chr11 135006516 6703555 0.0496535663508271 0.4917193629620151 chr12 133851895 6631258 0.04954175658103309 0.2657944142956439 chr13 115169878 4631134 0.04021133025772589 0.22761915627371587 chr14 107349540 4323401 0.04027405240860837 0.34380835550478533 chr15 102531392 4281033 0.04175338807455184 0.23860380181957977 chr16 90354753 4125372 0.045657498504810254 0.2880637523606018 chr17 81195210 3994741 0.04919922000324896 0.2957659286104131 chr18 78077248 3975093 0.05091230930680344 1.0991839073083929 chr19 59128983 3070017 0.051920679914281634 0.612994759228681 chr20 63025520 2972475 0.04716303808362073 0.2716941749858509 chr21 48129895 1864900 0.038747227684581484 0.2533844014797393 chr22 51304566 1597747 0.031142393836837055 0.20125574546321068 chrMT 16571 15786 0.9526280852091003 1.1655401069750462 chrX 155270560 8268830 0.05325433230871326 0.3778919814726595 chrY 59373566 411674 0.006933624300079938 0.20830706816683706