BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716210.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 = 1,397,965 number of mapped reads = 1,026,490 (73.43%) number of supplementary alignments = 25,459 (1.82%) number of secondary alignments = 0 number of mapped bases = 75,870,218 bp number of sequenced bases = 75,844,195 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,900 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7389 >>>>>>> ACTG content number of A's = 20,271,981 bp (26.73%) number of C's = 15,344,221 bp (20.23%) number of T's = 22,293,010 bp (29.39%) number of G's = 17,926,350 bp (23.64%) number of N's = 8,633 bp (0.01%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 557,773 number of insertions = 7,061 mapped reads with insertion percentage = 0.68% number of deletions = 14,559 mapped reads with deletion percentage = 1.4% homopolymer indels = 38.27% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2132X There is a 2.23% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5988745 0.024027001320891393 0.23253943393651255 chr2 243199373 6422567 0.026408649499273174 0.2865632123591535 chr3 198022430 5045602 0.02547995194281779 0.171110621304448 chr4 191154276 4829506 0.02526496451484036 0.18093518726230864 chr5 180915260 4506752 0.024910845000029297 0.1699595033258421 chr6 171115067 4456099 0.026041534963136822 0.18521009741026698 chr7 159138663 4148617 0.026069196019323098 0.2510130549201674 chr8 146364022 3847617 0.026287997196469497 0.2551755911881015 chr9 141213431 3222270 0.02281843856622958 0.2228978595242346 chr10 135534747 3681579 0.02716335907573576 0.2231788742506473 chr11 135006516 3409414 0.025253699606617507 0.2265500845668579 chr12 133851895 3485795 0.026042178932169768 0.17495982925794046 chr13 115169878 2369467 0.020573669445060973 0.1534841536428228 chr14 107349540 2363270 0.02201471939237001 0.18150185429585386 chr15 102531392 2189998 0.021359292576462827 0.15726670128885692 chr16 90354753 2325941 0.025742320384628797 0.181135695577741 chr17 81195210 2068104 0.025470763607853223 0.1814899462393118 chr18 78077248 2092565 0.026801213587855966 0.37760419898355585 chr19 59128983 1539707 0.026039801834575778 0.22245307972193598 chr20 63025520 1615507 0.025632585022701916 0.17955864278337774 chr21 48129895 1002621 0.0208315642492052 0.16605677990724588 chr22 51304566 898350 0.017510137401805525 0.14324650997400593 chrMT 16571 2926 0.17657353207410537 0.42897203677736856 chrX 155270560 4161942 0.02680445024478562 0.1991131016740765 chrY 59373566 195257 0.003288618372694677 0.10567024530743566