BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524944.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 = 1,583,157 number of mapped reads = 1,436,869 (90.76%) number of supplementary alignments = 4,955 (0.31%) number of secondary alignments = 0 number of mapped bases = 82,159,425 bp number of sequenced bases = 82,137,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,249 duplication rate = 1.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6394 >>>>>>> ACTG content number of A's = 21,276,259 bp (25.9%) number of C's = 15,998,989 bp (19.48%) number of T's = 25,676,330 bp (31.26%) number of G's = 19,184,030 bp (23.36%) number of N's = 2,343 bp (0%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 398,229 number of insertions = 5,506 mapped reads with insertion percentage = 0.38% number of deletions = 12,762 mapped reads with deletion percentage = 0.88% homopolymer indels = 41.62% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.2491X There is a 2.41% of reference with a coverageData >= 1X There is a 0.17% 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 5821021 0.023354088253204393 0.4062499233814183 chr2 243199373 6437255 0.02646904439182086 0.2774572670947369 chr3 198022430 4990069 0.025199514014649753 0.1694196141537798 chr4 191154276 5169226 0.027042167761918128 0.19412815719678192 chr5 180915260 4565913 0.025237854451857736 0.17121159079147222 chr6 171115067 4289798 0.025069668470515224 0.18343905092221063 chr7 159138663 5323808 0.033453894230593105 0.31822574176925117 chr8 146364022 3558860 0.0243151284815062 0.22908840106994965 chr9 141213431 3744501 0.02651660662504546 0.2595430166263813 chr10 135534747 3242113 0.02392089904443471 0.2446345380126223 chr11 135006516 3225717 0.023893046762276274 0.2156987652121266 chr12 133851895 6201463 0.046330782242567425 0.25566862721655964 chr13 115169878 3099920 0.026916065674741793 0.17451769027846872 chr14 107349540 2924087 0.027238933674052074 0.19468081922939864 chr15 102531392 2072057 0.020209000966260167 0.15328932100759893 chr16 90354753 2310389 0.02557019883613649 0.18885416138254218 chr17 81195210 2451651 0.03019452748505731 0.19382696543719843 chr18 78077248 2568710 0.03289959707596252 0.4560898310997819 chr19 59128983 1368892 0.02315094781860192 0.3327338424274235 chr20 63025520 2534759 0.0402179783681277 0.2215008393237656 chr21 48129895 993373 0.02063941755950226 0.17486427056502496 chr22 51304566 776133 0.015127951769439001 0.13012882336319825 chrMT 16571 2549 0.15382294369681976 0.40491409350591334 chrX 155270560 4253273 0.027392655761658873 0.20710234415839054 chrY 59373566 233888 0.0039392614551735025 0.10321923216369856