BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524943.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 = 1,263,336 number of mapped reads = 1,170,430 (92.65%) number of supplementary alignments = 3,077 (0.24%) number of secondary alignments = 0 number of mapped bases = 68,565,352 bp number of sequenced bases = 68,543,229 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,689 duplication rate = 1.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.762 >>>>>>> ACTG content number of A's = 16,733,126 bp (24.41%) number of C's = 12,100,747 bp (17.65%) number of T's = 22,384,275 bp (32.66%) number of G's = 17,324,281 bp (25.27%) number of N's = 800 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 331,317 number of insertions = 4,698 mapped reads with insertion percentage = 0.4% number of deletions = 12,983 mapped reads with deletion percentage = 1.1% homopolymer indels = 44.48% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.229X There is a 2.03% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7176708 0.028793139897533095 0.4347210018910089 chr2 243199373 5726742 0.02354751959002789 0.24179323856990537 chr3 198022430 3656298 0.018464059854229643 0.14422716262235982 chr4 191154276 4561766 0.023864315752999424 0.17852557925532409 chr5 180915260 2913961 0.01610677286150433 0.1368033175171064 chr6 171115067 4433882 0.02591169835441785 0.2354809328821431 chr7 159138663 4157168 0.02612292903327961 0.2898458021356008 chr8 146364022 4997113 0.03414167588261547 0.23998795633701758 chr9 141213431 2170607 0.01537110871557253 0.1835425428463914 chr10 135534747 3388264 0.024999227688822852 0.234502722258744 chr11 135006516 2757657 0.02042610298898462 0.20093416089735402 chr12 133851895 3841927 0.028702821129278744 0.18083569831278215 chr13 115169878 1378135 0.011966106276504001 0.11831363920849267 chr14 107349540 1833269 0.01707756735613399 0.1435911839005138 chr15 102531392 1948951 0.019008334540118212 0.15670831458574602 chr16 90354753 2148392 0.023777299241800817 0.17085714913942687 chr17 81195210 2257492 0.027803265734518082 0.2591621655679773 chr18 78077248 1360567 0.017425908761538315 0.2830924221097608 chr19 59128983 1486882 0.025146415929392867 0.2765777640340798 chr20 63025520 1435698 0.02277962958496812 0.1637077553841312 chr21 48129895 990230 0.020574115110785097 0.1653611437467288 chr22 51304566 906343 0.017665932501992124 0.13984807651277523 chrMT 16571 6218 0.37523384225454104 0.679916398985866 chrX 155270560 2834973 0.018258277679941388 0.1642127569135905 chrY 59373566 196109 0.0033029681929497043 0.09201976861637613