BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716641.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 = 855,466 number of mapped reads = 778,132 (90.96%) number of supplementary alignments = 2,498 (0.29%) number of secondary alignments = 0 number of mapped bases = 44,428,742 bp number of sequenced bases = 44,414,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,887 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9126 >>>>>>> ACTG content number of A's = 10,724,516 bp (24.15%) number of C's = 8,123,067 bp (18.29%) number of T's = 14,552,383 bp (32.76%) number of G's = 11,013,588 bp (24.8%) number of N's = 914 bp (0%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 229,950 number of insertions = 2,856 mapped reads with insertion percentage = 0.37% number of deletions = 8,767 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0144X std coverageData = 0.1658X There is a 1.34% of reference with a coverageData >= 1X There is a 0.06% 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 3746932 0.015032789025628946 0.23248468177908557 chr2 243199373 3563600 0.01465299830357704 0.240626655787684 chr3 198022430 2532041 0.012786637352142381 0.11963069330294439 chr4 191154276 2784641 0.014567505672747807 0.1418645863887534 chr5 180915260 2544165 0.01406274407145091 0.12399106471354744 chr6 171115067 2400307 0.014027443883711304 0.13853348004027716 chr7 159138663 2530481 0.01590110757685579 0.20887994553425976 chr8 146364022 2339926 0.015987029927341023 0.20565086990846218 chr9 141213431 1470598 0.010414009415294216 0.12074390136922299 chr10 135534747 1977318 0.014589011628139904 0.17444530525039104 chr11 135006516 1580781 0.011708923738169794 0.1302898580789024 chr12 133851895 2244603 0.016769303116702234 0.13694984124488713 chr13 115169878 1320350 0.011464369181670923 0.11305476147220127 chr14 107349540 1484760 0.013831079294797164 0.1237530064598704 chr15 102531392 1647591 0.016069137147772264 0.13280677422980258 chr16 90354753 1541353 0.017058903365050424 0.1402175171331057 chr17 81195210 1948601 0.02399896496357359 0.16554521083634946 chr18 78077248 834928 0.010693614611006782 0.17205974575805222 chr19 59128983 1107500 0.018730239280455745 0.20613811928771583 chr20 63025520 1301267 0.020646668206783538 0.1533716574853597 chr21 48129895 560725 0.01165024357522492 0.1351956262138833 chr22 51304566 414754 0.008084153757386818 0.09420067889044395 chrMT 16571 32364 1.9530505099269808 1.7414720701925746 chrX 155270560 2344998 0.015102656936382531 0.13575893448905574 chrY 59373566 174158 0.0029332582112383144 0.1336971737534404