BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751179.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,132,945 number of mapped reads = 4,115,437 (99.58%) number of supplementary alignments = 27,369 (0.66%) number of secondary alignments = 0 number of mapped bases = 399,475,659 bp number of sequenced bases = 399,385,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 649,536 duplication rate = 10.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9553 >>>>>>> ACTG content number of A's = 122,907,892 bp (30.77%) number of C's = 77,217,989 bp (19.33%) number of T's = 123,488,313 bp (30.92%) number of G's = 75,768,743 bp (18.97%) number of N's = 2,896 bp (0%) GC percentage = 38.31% >>>>>>> Mismatches and indels general error rate = 0.0023 number of mismatches = 843,955 number of insertions = 35,998 mapped reads with insertion percentage = 0.87% number of deletions = 43,226 mapped reads with deletion percentage = 1.04% homopolymer indels = 48.13% >>>>>>> Coverage mean coverageData = 0.129X std coverageData = 1.6802X There is a 4.74% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 30018894 0.12043658659530482 1.2144880377631195 chr2 243199373 23493656 0.09660245300056756 1.023663857930186 chr3 198022430 30544982 0.154250111969639 1.8458058548063654 chr4 191154276 29731601 0.1555372007477353 1.7714323373040324 chr5 180915260 33274154 0.18392121261633762 1.1730024580674556 chr6 171115067 24343423 0.14226346882709048 1.6821090842471385 chr7 159138663 25543128 0.16050862511016573 1.7290126057086963 chr8 146364022 21634452 0.14781263663279218 1.5403824878958632 chr9 141213431 19617314 0.13891960460899785 2.5210660309349118 chr10 135534747 17058420 0.1258601235297986 1.5970493859484505 chr11 135006516 22330909 0.1654061571368896 1.7921958646184726 chr12 133851895 30927892 0.23106054643454993 3.348652619770479 chr13 115169878 27054610 0.23491046851677658 3.0500222540962394 chr14 107349540 8817554 0.08213872178679107 1.7150527931639632 chr15 102531392 7234469 0.07055857585548043 1.1545753388759497 chr16 90354753 6441369 0.07128976380467777 0.8372741598203343 chr17 81195210 4292766 0.05286969514580971 0.5418727424453221 chr18 78077248 7832784 0.10032095393526165 1.0092206257024205 chr19 59128983 1268678 0.021456110618374748 0.20218389969255457 chr20 63025520 3915968 0.06213305340439872 0.6336805520303629 chr21 48129895 2127389 0.044200989842176054 0.3745989622262257 chr22 51304566 1700003 0.0331355107847516 0.6374667783030662 chrMT 16571 5111 0.3084303904411321 0.5431483171374385 chrX 155270560 20059631 0.12919146424151495 1.5088437797884227 chrY 59373566 206502 0.0034780124205441862 0.08310078781077629