BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173922.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,928,340 number of mapped reads = 1,865,685 (96.75%) number of supplementary alignments = 190,762 (9.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 934,865 number of mapped paired reads (second in pair) = 930,820 number of mapped paired reads (both in pair) = 1,826,932 number of mapped paired reads (singletons) = 38,753 number of mapped bases = 219,867,991 bp number of sequenced bases = 219,740,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,455,061 duplication rate = 63.82% >>>>>>> Insert size mean insert size = 1,230,829.6451 std insert size = 10,529,691.6131 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 52.808 >>>>>>> ACTG content number of A's = 66,254,667 bp (30.15%) number of C's = 42,900,268 bp (19.52%) number of T's = 65,999,904 bp (30.04%) number of G's = 44,582,904 bp (20.29%) number of N's = 2,683 bp (0%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 2,431,976 number of insertions = 26,974 mapped reads with insertion percentage = 1.38% number of deletions = 49,976 mapped reads with deletion percentage = 2.6% homopolymer indels = 42.57% >>>>>>> Coverage mean coverageData = 0.071X std coverageData = 1.2208X There is a 1.49% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 17223960 0.06910297728004457 0.9852522793647307 chr2 243199373 20481541 0.08421707978663251 3.1642549528408717 chr3 198022430 15204768 0.07678305937362752 0.8063000134130359 chr4 191154276 15078712 0.07888242060564735 1.0380745408665706 chr5 180915260 13991595 0.07733783761524594 0.8137089798910607 chr6 171115067 13132282 0.07674532833511383 0.8414190083843889 chr7 159138663 11972054 0.07523032916268751 0.9167407131882089 chr8 146364022 11216572 0.07663476205921699 1.0186554038625073 chr9 141213431 9324882 0.06603395961677327 0.8962326411875327 chr10 135534747 10741439 0.07925228945164889 1.095486448316211 chr11 135006516 10195069 0.07551538475372552 0.8093083966237781 chr12 133851895 10068765 0.07522317857360182 0.7967631214240933 chr13 115169878 7210236 0.06260522391106466 0.7314431543331986 chr14 107349540 6591212 0.06139953650476751 0.713512870162984 chr15 102531392 6452032 0.06292738130386448 0.7175265200570475 chr16 90354753 6497317 0.0719089675337832 0.8481986163119716 chr17 81195210 5887922 0.0725156323876741 0.7948369276851769 chr18 78077248 6332214 0.08110191076406792 1.2211495140146362 chr19 59128983 3789558 0.06408968677847884 0.7805905948119621 chr20 63025520 4610122 0.07314690937893095 0.7902335503185097 chr21 48129895 3348205 0.06956601505155995 0.8934787713962734 chr22 51304566 2624063 0.05114677317414594 0.6537001734910338 chrMT 16571 394572 23.81099511194255 20.21305235497878 chrX 155270560 5689809 0.0366444804475491 0.5436007617811247 chrY 59373566 1809090 0.030469620099961656 0.6618508288453702