BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004077.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,333,375 number of mapped reads = 2,087,019 (89.44%) number of supplementary alignments = 12,557 (0.54%) number of secondary alignments = 0 number of mapped bases = 139,137,767 bp number of sequenced bases = 139,080,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,365 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.273 >>>>>>> ACTG content number of A's = 38,311,142 bp (27.55%) number of C's = 26,344,512 bp (18.94%) number of T's = 42,855,157 bp (30.81%) number of G's = 31,544,716 bp (22.68%) number of N's = 24,861 bp (0.02%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,172,698 number of insertions = 9,823 mapped reads with insertion percentage = 0.47% number of deletions = 33,015 mapped reads with deletion percentage = 1.57% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.0449X std coverageData = 0.3595X There is a 3.89% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 12291118 0.04931228636738281 0.6164959568139098 chr2 243199373 10199015 0.0419368474276453 0.41315307388461814 chr3 198022430 8720385 0.044037359808179306 0.23332352516446184 chr4 191154276 7894601 0.041299630671092075 0.24038715242247483 chr5 180915260 9161803 0.05064140526343659 0.25332812373681773 chr6 171115067 9783787 0.05717665411661265 0.2992333272149979 chr7 159138663 8740121 0.05492141780781456 0.6659321470919712 chr8 146364022 10310307 0.07044290570260497 0.41941876938061884 chr9 141213431 4319489 0.030588372291584644 0.2709781601765873 chr10 135534747 5557801 0.04100646603929544 0.2914132993063402 chr11 135006516 4145388 0.03070509574515648 0.23445437038330624 chr12 133851895 5735974 0.042853140032122816 0.23263130895971515 chr13 115169878 4710670 0.04090192749878575 0.23841241856990983 chr14 107349540 3417020 0.031830783811463 0.2138269260445495 chr15 102531392 5527632 0.05391160592065306 0.26926681287233206 chr16 90354753 3411122 0.037752546343632856 0.23029316559367502 chr17 81195210 3993208 0.049180339579145124 0.2642850112901359 chr18 78077248 3606367 0.046189729945399716 0.478523255261111 chr19 59128983 2778603 0.04699223391006065 0.474151136314794 chr20 63025520 2318951 0.03679384160574954 0.2227355637249347 chr21 48129895 1469010 0.030521778615972463 0.2057831197219559 chr22 51304566 1000924 0.019509452628446364 0.1526847323106171 chrMT 16571 28779 1.7367087079838273 1.8968781294292487 chrX 155270560 9673120 0.062298480793783445 0.3013172466208698 chrY 59373566 342572 0.005769773033339449 0.10963129224301