BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818871.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 804,183 number of mapped reads = 792,952 (98.6%) number of supplementary alignments = 12,731 (1.58%) number of secondary alignments = 0 number of mapped bases = 73,375,363 bp number of sequenced bases = 73,330,935 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,580 duplication rate = 14.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4005 >>>>>>> ACTG content number of A's = 21,372,212 bp (29.14%) number of C's = 15,593,439 bp (21.26%) number of T's = 20,620,963 bp (28.12%) number of G's = 15,743,248 bp (21.47%) number of N's = 1,073 bp (0%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 435,837 number of insertions = 9,303 mapped reads with insertion percentage = 1.14% number of deletions = 23,727 mapped reads with deletion percentage = 2.92% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2953X There is a 1.82% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6879184 0.027599465840448197 0.41489831505281993 chr2 243199373 5542386 0.022789474872535957 0.390304658723746 chr3 198022430 4680668 0.023637059700762183 0.19045327302649304 chr4 191154276 3833031 0.020052028551011854 0.20912199072473675 chr5 180915260 3277322 0.018115232512724466 0.16889591899723808 chr6 171115067 3682663 0.021521558940218864 0.19258679695104178 chr7 159138663 6549384 0.04115520311993572 0.5988027360474297 chr8 146364022 6538114 0.04467022640304323 0.29663037060172387 chr9 141213431 2682430 0.018995572736987036 0.25115949683741 chr10 135534747 3396231 0.025058009663012835 0.36398591743983755 chr11 135006516 3250551 0.024076993439338883 0.2106805056534192 chr12 133851895 2822708 0.021088293146690227 0.18149275912692578 chr13 115169878 2311390 0.020069396965064077 0.17677831826133011 chr14 107349540 2113098 0.019684276243754746 0.17981352286923974 chr15 102531392 2015780 0.019660125164398433 0.1741891761764613 chr16 90354753 1739826 0.019255500593311346 0.27163712928122374 chr17 81195210 1724101 0.021234023534146905 0.20732479916308882 chr18 78077248 1417081 0.018149730379841255 0.2691960465394541 chr19 59128983 1175120 0.01987384088780962 0.3679728196791514 chr20 63025520 2940772 0.04666001962379684 0.2791549520509537 chr21 48129895 688053 0.014295751112692018 0.1613146487952403 chr22 51304566 641562 0.012504968855988374 0.14935280406647017 chrMT 16571 184470 11.132098243920101 8.872052746044776 chrX 155270560 3036121 0.01955374541059168 0.1914563519062482 chrY 59373566 253317 0.004266494621529049 0.29471499794676503