BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438291.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 703,325,588 number of mapped reads = 701,179,152 (99.69%) number of supplementary alignments = 11,569,711 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 350,700,128 number of mapped paired reads (second in pair) = 350,479,024 number of mapped paired reads (both in pair) = 699,705,910 number of mapped paired reads (singletons) = 1,473,242 number of mapped bases = 100,995,931,964 bp number of sequenced bases = 100,968,618,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 339,716,271 duplication rate = 45.6% >>>>>>> Insert size mean insert size = 39,426.6417 std insert size = 1,937,538.7579 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 55.1358 >>>>>>> ACTG content number of A's = 30,550,907,872 bp (30.26%) number of C's = 20,176,426,979 bp (19.98%) number of T's = 29,225,887,551 bp (28.95%) number of G's = 21,014,774,625 bp (20.81%) number of N's = 621,525 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 514,660,025 number of insertions = 12,616,301 mapped reads with insertion percentage = 1.77% number of deletions = 11,163,279 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 32.6246X std coverageData = 83.4599X There is a 90.99% of reference with a coverageData >= 1X There is a 90.07% of reference with a coverageData >= 2X There is a 89% of reference with a coverageData >= 3X There is a 87.86% of reference with a coverageData >= 4X There is a 86.59% of reference with a coverageData >= 5X There is a 85.23% of reference with a coverageData >= 6X There is a 83.76% of reference with a coverageData >= 7X There is a 82.22% of reference with a coverageData >= 8X There is a 80.59% of reference with a coverageData >= 9X There is a 78.9% of reference with a coverageData >= 10X There is a 77.16% of reference with a coverageData >= 11X There is a 75.37% of reference with a coverageData >= 12X There is a 73.55% of reference with a coverageData >= 13X There is a 71.7% of reference with a coverageData >= 14X There is a 69.83% of reference with a coverageData >= 15X There is a 67.95% of reference with a coverageData >= 16X There is a 66.07% of reference with a coverageData >= 17X There is a 64.19% of reference with a coverageData >= 18X There is a 62.33% of reference with a coverageData >= 19X There is a 60.47% of reference with a coverageData >= 20X There is a 58.64% of reference with a coverageData >= 21X There is a 56.82% of reference with a coverageData >= 22X There is a 55.04% of reference with a coverageData >= 23X There is a 53.29% of reference with a coverageData >= 24X There is a 51.56% of reference with a coverageData >= 25X There is a 49.87% of reference with a coverageData >= 26X There is a 48.22% of reference with a coverageData >= 27X There is a 46.6% of reference with a coverageData >= 28X There is a 45.03% of reference with a coverageData >= 29X There is a 43.49% of reference with a coverageData >= 30X There is a 41.99% of reference with a coverageData >= 31X There is a 40.54% of reference with a coverageData >= 32X There is a 39.12% of reference with a coverageData >= 33X There is a 37.75% of reference with a coverageData >= 34X There is a 36.42% of reference with a coverageData >= 35X There is a 35.12% of reference with a coverageData >= 36X There is a 33.87% of reference with a coverageData >= 37X There is a 32.65% of reference with a coverageData >= 38X There is a 31.48% of reference with a coverageData >= 39X There is a 30.34% of reference with a coverageData >= 40X There is a 29.25% of reference with a coverageData >= 41X There is a 28.19% of reference with a coverageData >= 42X There is a 27.16% of reference with a coverageData >= 43X There is a 26.17% of reference with a coverageData >= 44X There is a 25.22% of reference with a coverageData >= 45X There is a 24.3% of reference with a coverageData >= 46X There is a 23.41% of reference with a coverageData >= 47X There is a 22.55% of reference with a coverageData >= 48X There is a 21.73% of reference with a coverageData >= 49X There is a 20.93% of reference with a coverageData >= 50X There is a 20.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8271242452 33.18444069994915 33.85572250506155 chr2 243199373 8918776744 36.67269629021617 130.28433222601717 chr3 198022430 7070450393 35.7053006217528 56.262883857365 chr4 191154276 6796591176 35.55552780833425 29.237041405517914 chr5 180915260 6427762582 35.52913436931744 30.3729653539575 chr6 171115067 6209515440 36.28853699949169 30.876003589983974 chr7 159138663 5340618360 33.55952764288337 29.996412133022016 chr8 146364022 5387341996 36.80782970011578 31.022501385062142 chr9 141213431 4412837485 31.249417663394922 35.35801433496633 chr10 135534747 4835483464 35.67707596045463 36.696937133811254 chr11 135006516 4964659942 36.77348389614024 32.34154247857603 chr12 133851895 4768149323 35.62257615403951 30.078714672129443 chr13 115169878 3574304152 31.035060677931778 30.028612175367446 chr14 107349540 3268404042 30.446372122321158 31.018625713762223 chr15 102531392 2856934838 27.86400128070045 30.832354066059775 chr16 90354753 2567807703 28.41917683068648 49.64203964047537 chr17 81195210 2425382445 29.871004028439607 37.180628773560976 chr18 78077248 2801795849 35.884920649354854 31.657605338258584 chr19 59128983 1565891241 26.482634429886946 74.07823965770683 chr20 63025520 2156636645 34.21846650372738 32.27188977259875 chr21 48129895 1285119986 26.701076036006313 38.62222349008296 chr22 51304566 1002301291 19.536298016827587 28.387336276733652 chrMT 16571 444941579 26850.6172832056 10365.090410072702 chrX 155270560 3170094803 20.416586396030258 21.16030052067675 chrY 59373566 472888033 7.964622387680066 25.79903142942403