BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524820.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 = 1,839,000 number of mapped reads = 1,687,818 (91.78%) number of supplementary alignments = 6,015 (0.33%) number of secondary alignments = 0 number of mapped bases = 97,253,359 bp number of sequenced bases = 97,223,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,068 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5871 >>>>>>> ACTG content number of A's = 23,431,385 bp (24.1%) number of C's = 19,114,006 bp (19.66%) number of T's = 30,230,596 bp (31.09%) number of G's = 24,435,935 bp (25.13%) number of N's = 11,228 bp (0.01%) GC percentage = 44.79% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 480,946 number of insertions = 6,195 mapped reads with insertion percentage = 0.36% number of deletions = 18,632 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.2582X There is a 2.76% of reference with a coverageData >= 1X There is a 0.27% 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 7770169 0.031174120926262407 0.3078428056573921 chr2 243199373 8172528 0.03360423137275111 0.39856712272744504 chr3 198022430 6311533 0.03187281864988729 0.20179518551545128 chr4 191154276 6176367 0.03231090158820198 0.24789119283594938 chr5 180915260 5780463 0.03195121848759469 0.19923044999635442 chr6 171115067 5466908 0.031948723720512585 0.21793049883967233 chr7 159138663 5353909 0.0336430437397856 0.30383383401158626 chr8 146364022 4875302 0.03330942900708208 0.23612478890664898 chr9 141213431 4112072 0.029119553082737577 0.2294585634749273 chr10 135534747 4739604 0.03496965984671075 0.34139365982323455 chr11 135006516 4390018 0.032517082360676575 0.23698407490495774 chr12 133851895 4398393 0.03286014740396466 0.2031688033650383 chr13 115169878 2979149 0.025867432107551595 0.17888172737934463 chr14 107349540 2901318 0.02702683215969067 0.18537618254417157 chr15 102531392 2820770 0.027511281618023874 0.18534711028844195 chr16 90354753 3022086 0.03344689570453477 0.23532576150429013 chr17 81195210 2864778 0.03528259856708296 0.2198053030375304 chr18 78077248 2518044 0.03225067563856759 0.33853837259732766 chr19 59128983 2206967 0.037324623019475915 0.2758447311616834 chr20 63025520 2156846 0.034221788253393226 0.22386137947011853 chr21 48129895 1295468 0.026916077834784388 0.21598368638064885 chr22 51304566 1263420 0.024625878328256398 0.17727906333017304 chrMT 16571 27299 1.6473960533462073 1.7632864868823783 chrX 155270560 5313944 0.03422377043014464 0.22011789792252914 chrY 59373566 336004 0.0056591514142842626 0.1762516070804117