BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008809.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 797,542 number of mapped reads = 689,472 (86.45%) number of supplementary alignments = 6,365 (0.8%) number of secondary alignments = 0 number of mapped bases = 44,910,887 bp number of sequenced bases = 44,886,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,599 duplication rate = 5.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9126 >>>>>>> ACTG content number of A's = 12,196,179 bp (27.17%) number of C's = 8,665,415 bp (19.31%) number of T's = 13,825,877 bp (30.8%) number of G's = 10,143,389 bp (22.6%) number of N's = 55,362 bp (0.12%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 382,869 number of insertions = 3,303 mapped reads with insertion percentage = 0.48% number of deletions = 13,985 mapped reads with deletion percentage = 2.01% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1909X There is a 1.09% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 3429651 0.013759849368640088 0.2449733245922502 chr2 243199373 3432091 0.014112252666046142 0.22897588808702868 chr3 198022430 3558859 0.017971999434609504 0.17253552005018857 chr4 191154276 2704058 0.014145945654911743 0.15456622881756643 chr5 180915260 3162301 0.017479459720534354 0.1685700697572312 chr6 171115067 3146127 0.01838603142995 0.18205590224913532 chr7 159138663 1666598 0.010472615319132095 0.236998921246808 chr8 146364022 1669416 0.01140591777397317 0.27956226088799035 chr9 141213431 1591918 0.01127313449384287 0.15084012452033796 chr10 135534747 2873550 0.021201574235424663 0.23623535865088127 chr11 135006516 1943017 0.014392023863500041 0.15880457585206592 chr12 133851895 2062580 0.015409419493089731 0.15945229866500726 chr13 115169878 1477840 0.012831827433211313 0.14407981131557884 chr14 107349540 1221956 0.011382964472879903 0.13914716875046917 chr15 102531392 1270533 0.012391648793766499 0.14071256713949432 chr16 90354753 1454068 0.016092877814629186 0.17928737803261452 chr17 81195210 1465174 0.018045079260217443 0.17517272627230243 chr18 78077248 1028078 0.013167446680497755 0.18741696328254606 chr19 59128983 1000426 0.01691938452585934 0.22745900835781838 chr20 63025520 1158627 0.018383458002409182 0.17497497925766978 chr21 48129895 443821 0.009221316605822639 0.12523213229902447 chr22 51304566 441459 0.008604672730298508 0.11781177922801926 chrMT 16571 13357 0.80604670810452 1.2880550799980286 chrX 155270560 2570799 0.016556899131425815 0.16667732927801382 chrY 59373566 124583 0.002098290677032941 0.07886253569877721