BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524545.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 = 1,810,377 number of mapped reads = 1,650,346 (91.16%) number of supplementary alignments = 5,680 (0.31%) number of secondary alignments = 0 number of mapped bases = 95,609,599 bp number of sequenced bases = 95,580,966 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,945 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8017 >>>>>>> ACTG content number of A's = 23,404,633 bp (24.49%) number of C's = 16,988,472 bp (17.77%) number of T's = 31,608,210 bp (33.07%) number of G's = 23,578,289 bp (24.67%) number of N's = 1,362 bp (0%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 488,798 number of insertions = 6,623 mapped reads with insertion percentage = 0.4% number of deletions = 17,309 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.16% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.294X There is a 2.71% 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 9315372 0.037373515711320936 0.5618454591382053 chr2 243199373 7482159 0.03076553573187049 0.33536859996519763 chr3 198022430 5132442 0.02591848812278488 0.18239427140013673 chr4 191154276 5413905 0.028322175748765357 0.21793184647201982 chr5 180915260 5258064 0.029063684290645243 0.19076379248185882 chr6 171115067 4062095 0.023738967416586407 0.219772107402329 chr7 159138663 4787264 0.0300823439744495 0.35481634693867226 chr8 146364022 9102507 0.062190877755463704 0.331075513311079 chr9 141213431 4034835 0.028572600859758164 0.24712263729556286 chr10 135534747 4910156 0.036228023504555625 0.29411688581983814 chr11 135006516 3258925 0.024139020075149557 0.26727156076617264 chr12 133851895 4473373 0.033420318778452855 0.20546743128069556 chr13 115169878 2110113 0.01832174381568764 0.1512633308911303 chr14 107349540 2272658 0.021170635663646065 0.1672378800988043 chr15 102531392 2516803 0.02454665786650005 0.17859870762991303 chr16 90354753 2998374 0.03318446346701872 0.2194055087568593 chr17 81195210 3348996 0.04124622622442876 0.2380836884080375 chr18 78077248 2245630 0.02876164385302105 0.4495773383792203 chr19 59128983 2028836 0.03431203949508146 0.3825661494927042 chr20 63025520 2688734 0.04266103635479723 0.23458025047142633 chr21 48129895 1341847 0.02787969930123471 0.20673963887712907 chr22 51304566 822027 0.016022492033165234 0.1397373881050913 chrMT 16571 6611 0.39894997284412526 0.7536901566138606 chrX 155270560 5673393 0.03653875531845831 0.23378191328888467 chrY 59373566 324480 0.005465058305576593 0.1700332251858766