BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212164.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,462,974 number of mapped reads = 3,924,340 (87.93%) number of supplementary alignments = 33,017 (0.74%) number of secondary alignments = 0 number of mapped bases = 268,102,205 bp number of sequenced bases = 267,982,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 172,579 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3706 >>>>>>> ACTG content number of A's = 74,774,861 bp (27.9%) number of C's = 49,386,524 bp (18.43%) number of T's = 85,215,548 bp (31.8%) number of G's = 58,532,922 bp (21.84%) number of N's = 72,196 bp (0.03%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,344,762 number of insertions = 22,527 mapped reads with insertion percentage = 0.57% number of deletions = 71,557 mapped reads with deletion percentage = 1.8% homopolymer indels = 49.34% >>>>>>> Coverage mean coverageData = 0.0866X std coverageData = 0.7203X There is a 6.97% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 26986123 0.10826903015017965 1.4593506364936024 chr2 243199373 16822328 0.06917093491026394 0.7698635637163604 chr3 198022430 16204864 0.08183347714700805 0.34746811888574725 chr4 191154276 12117033 0.06338876248836829 0.34782782604828366 chr5 180915260 19769653 0.10927576258630699 0.39582070443342193 chr6 171115067 18347835 0.1072251282232207 0.5190916639622096 chr7 159138663 15270711 0.09595852266271711 0.7777866761712102 chr8 146364022 15403379 0.10524020035470193 1.007414553953723 chr9 141213431 10098608 0.07151308433260856 0.686509304854376 chr10 135534747 8068414 0.05953022511636813 0.759545958575684 chr11 135006516 14273267 0.10572280081651762 0.7981519423339607 chr12 133851895 6430580 0.048042502498750576 0.28064351838637674 chr13 115169878 8261726 0.0717351285203237 0.3124522911395664 chr14 107349540 9805638 0.0913430835381316 0.4147007700422698 chr15 102531392 8020539 0.07822520345768835 0.3281626621494201 chr16 90354753 8811231 0.09751817925947957 0.436497365823472 chr17 81195210 4521538 0.05568725051637898 0.4125295090992801 chr18 78077248 8935037 0.1144384212927177 1.202125988067445 chr19 59128983 6732026 0.11385323505394977 1.1168599208632266 chr20 63025520 6637003 0.10530659643902977 0.4110325424571377 chr21 48129895 4425821 0.09195575847402118 0.4312607657330122 chr22 51304566 1827713 0.035624762910965856 0.21743577660346675 chrMT 16571 8894 0.5367207772614809 0.8664488068619989 chrX 155270560 19573844 0.12606281577138642 0.4882341434260428 chrY 59373566 748400 0.012604936008054493 0.26413208620429585