BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716478.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 = 1,160,820 number of mapped reads = 1,005,344 (86.61%) number of supplementary alignments = 5,193 (0.45%) number of secondary alignments = 0 number of mapped bases = 58,485,936 bp number of sequenced bases = 58,468,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,136 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7079 >>>>>>> ACTG content number of A's = 15,090,689 bp (25.81%) number of C's = 11,177,914 bp (19.12%) number of T's = 18,475,572 bp (31.6%) number of G's = 13,724,299 bp (23.47%) number of N's = 413 bp (0%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 290,858 number of insertions = 4,659 mapped reads with insertion percentage = 0.46% number of deletions = 10,631 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.51% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.193X There is a 1.73% 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 7206581 0.028912991153590747 0.30246432666859496 chr2 243199373 5965146 0.02452780172258092 0.267602163217425 chr3 198022430 3641872 0.01839120952106284 0.14515864403196224 chr4 191154276 2455193 0.012844039125758296 0.13562662825078434 chr5 180915260 4182421 0.023118121710683774 0.16324379156868404 chr6 171115067 2107534 0.012316472400411123 0.12830216250620738 chr7 159138663 3819001 0.023997945741193013 0.26688423175501047 chr8 146364022 2609966 0.01783201885501616 0.18757538383120806 chr9 141213431 1619805 0.01147061570935133 0.1466180927729955 chr10 135534747 2606200 0.019229017338262343 0.17724502614721238 chr11 135006516 2510106 0.018592480380724734 0.18898405423057718 chr12 133851895 2347498 0.017538025890481417 0.1425131351622993 chr13 115169878 1657652 0.01439310372456937 0.1293641025603752 chr14 107349540 1239533 0.011546700619304004 0.11863945771336407 chr15 102531392 2520183 0.024579623380125377 0.16834729045121405 chr16 90354753 1691232 0.018717687159191282 0.1530163232121935 chr17 81195210 2212484 0.02724894732090723 0.18668917881015978 chr18 78077248 1842444 0.023597706722450054 0.31048683728038845 chr19 59128983 925393 0.015650412928630956 0.21026111781359513 chr20 63025520 1510849 0.023972019588255677 0.16883558986658231 chr21 48129895 754984 0.015686383691466604 0.14348783649953228 chr22 51304566 741773 0.014458225803917726 0.12842785773237955 chrMT 16571 3978 0.2400579325327379 0.5101119643447863 chrX 155270560 2167056 0.013956644453397992 0.1389838840168867 chrY 59373566 147052 0.0024767250799791946 0.07340066171032257