BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438281.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 = 608,792,864 number of mapped reads = 606,661,749 (99.65%) number of supplementary alignments = 9,795,655 (1.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 303,632,693 number of mapped paired reads (second in pair) = 303,029,056 number of mapped paired reads (both in pair) = 605,112,208 number of mapped paired reads (singletons) = 1,549,541 number of mapped bases = 87,793,203,472 bp number of sequenced bases = 87,766,627,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 262,101,496 duplication rate = 40.82% >>>>>>> Insert size mean insert size = 39,218.8028 std insert size = 1,911,358.0931 median insert size = 266 >>>>>>> Mapping quality mean mapping quality = 55.0009 >>>>>>> ACTG content number of A's = 26,637,758,656 bp (30.35%) number of C's = 17,431,674,921 bp (19.86%) number of T's = 25,310,459,584 bp (28.84%) number of G's = 18,386,078,731 bp (20.95%) number of N's = 655,903 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 455,681,533 number of insertions = 11,840,504 mapped reads with insertion percentage = 1.92% number of deletions = 10,453,274 mapped reads with deletion percentage = 1.69% homopolymer indels = 48.59% >>>>>>> Coverage mean coverageData = 28.3598X std coverageData = 74.4293X There is a 91.35% of reference with a coverageData >= 1X There is a 90.55% of reference with a coverageData >= 2X There is a 89.6% of reference with a coverageData >= 3X There is a 88.54% of reference with a coverageData >= 4X There is a 87.32% of reference with a coverageData >= 5X There is a 85.97% of reference with a coverageData >= 6X There is a 84.48% of reference with a coverageData >= 7X There is a 82.85% of reference with a coverageData >= 8X There is a 81.11% of reference with a coverageData >= 9X There is a 79.25% of reference with a coverageData >= 10X There is a 77.3% of reference with a coverageData >= 11X There is a 75.28% of reference with a coverageData >= 12X There is a 73.18% of reference with a coverageData >= 13X There is a 71.03% of reference with a coverageData >= 14X There is a 68.85% of reference with a coverageData >= 15X There is a 66.64% of reference with a coverageData >= 16X There is a 64.41% of reference with a coverageData >= 17X There is a 62.19% of reference with a coverageData >= 18X There is a 59.97% of reference with a coverageData >= 19X There is a 57.77% of reference with a coverageData >= 20X There is a 55.6% of reference with a coverageData >= 21X There is a 53.46% of reference with a coverageData >= 22X There is a 51.36% of reference with a coverageData >= 23X There is a 49.3% of reference with a coverageData >= 24X There is a 47.29% of reference with a coverageData >= 25X There is a 45.34% of reference with a coverageData >= 26X There is a 43.43% of reference with a coverageData >= 27X There is a 41.59% of reference with a coverageData >= 28X There is a 39.8% of reference with a coverageData >= 29X There is a 38.07% of reference with a coverageData >= 30X There is a 36.4% of reference with a coverageData >= 31X There is a 34.8% of reference with a coverageData >= 32X There is a 33.25% of reference with a coverageData >= 33X There is a 31.76% of reference with a coverageData >= 34X There is a 30.33% of reference with a coverageData >= 35X There is a 28.96% of reference with a coverageData >= 36X There is a 27.64% of reference with a coverageData >= 37X There is a 26.38% of reference with a coverageData >= 38X There is a 25.17% of reference with a coverageData >= 39X There is a 24.01% of reference with a coverageData >= 40X There is a 22.9% of reference with a coverageData >= 41X There is a 21.85% of reference with a coverageData >= 42X There is a 20.84% of reference with a coverageData >= 43X There is a 19.87% of reference with a coverageData >= 44X There is a 18.95% of reference with a coverageData >= 45X There is a 18.07% of reference with a coverageData >= 46X There is a 17.23% of reference with a coverageData >= 47X There is a 16.43% of reference with a coverageData >= 48X There is a 15.67% of reference with a coverageData >= 49X There is a 14.94% of reference with a coverageData >= 50X There is a 14.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7161522912 28.732216927957023 30.178694678332327 chr2 243199373 7647901948 31.447046321126823 73.25928076094033 chr3 198022430 6236314755 31.492971553778023 49.87662737830871 chr4 191154276 5967768005 31.21964169402101 23.619364681837748 chr5 180915260 5781021048 31.95430306984607 24.301154079701682 chr6 171115067 5363307927 31.343282745522345 25.742281229983732 chr7 159138663 4717548195 29.64426184100843 24.208239841586106 chr8 146364022 4624370381 31.594993891326656 24.51157431561332 chr9 141213431 3824364529 27.08215855898296 32.51514319281408 chr10 135534747 4100158802 30.25171694163416 40.167730878592096 chr11 135006516 4129612841 30.588248355360864 25.12463361728595 chr12 133851895 4147167791 30.98325795835763 24.066200610771233 chr13 115169878 3063229568 26.597489041362014 24.332650442651197 chr14 107349540 2828923522 26.352451272730185 26.293383448567795 chr15 102531392 2573262215 25.097310831398836 25.88674704954603 chr16 90354753 2340558136 25.904095338515287 47.53731421275743 chr17 81195210 2073802887 25.540951085661334 30.638048653776952 chr18 78077248 2383359077 30.525654246932472 26.772511242059522 chr19 59128983 1356536139 22.941983274090813 59.40904940363158 chr20 63025520 1841207551 29.213682822450334 26.230478374857196 chr21 48129895 1098192063 22.817254494322086 36.5099521980685 chr22 51304566 969357274 18.894171602582116 25.127028612486583 chrMT 16571 430383576 25972.094381751253 10650.54702831334 chrX 155270560 2666879298 17.17569188904838 17.150871765818675 chrY 59373566 466453032 7.8562408058832105 26.925561423390043