BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240227.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 = 1,500,628 number of mapped reads = 1,007,013 (67.11%) number of supplementary alignments = 7,169 (0.48%) number of secondary alignments = 0 number of mapped bases = 61,890,055 bp number of sequenced bases = 61,860,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 270,406 duplication rate = 16.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1222 >>>>>>> ACTG content number of A's = 16,772,307 bp (27.11%) number of C's = 10,896,172 bp (17.61%) number of T's = 20,173,084 bp (32.61%) number of G's = 14,004,136 bp (22.64%) number of N's = 14,689 bp (0.02%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 546,087 number of insertions = 4,264 mapped reads with insertion percentage = 0.42% number of deletions = 17,341 mapped reads with deletion percentage = 1.7% homopolymer indels = 49.57% >>>>>>> Coverage mean coverageData = 0.02X std coverageData = 0.345X There is a 0.72% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 4946194 0.019844259485315385 0.39576217185851675 chr2 243199373 5967152 0.024536050099109426 0.40510985276752326 chr3 198022430 4085091 0.020629435766443226 0.33083923203011995 chr4 191154276 4698217 0.024578142316837318 0.3681404963208797 chr5 180915260 3228565 0.017845730647597112 0.2962031029289909 chr6 171115067 3408177 0.019917457064140356 0.33041275260940606 chr7 159138663 4474202 0.028115116186441757 0.4455551325744736 chr8 146364022 3355316 0.022924458853692882 0.4270098897725977 chr9 141213431 2905315 0.020573928268905244 0.33595524336380506 chr10 135534747 2926648 0.02159334093123736 0.34075266798513726 chr11 135006516 2449940 0.018146827816814412 0.322844252925811 chr12 133851895 2974976 0.022225878834214487 0.3286275129500266 chr13 115169878 1874276 0.016274012203086646 0.28756891081557767 chr14 107349540 1689901 0.015742042304047136 0.2870477396820438 chr15 102531392 1477440 0.014409635636274206 0.26213400080656585 chr16 90354753 1508284 0.016692912657289873 0.2779891173753825 chr17 81195210 1302782 0.01604505980094146 0.2691370158480137 chr18 78077248 1553057 0.019891287664237346 0.4142158758928008 chr19 59128983 981053 0.01659174486393585 0.3097319745294697 chr20 63025520 1093090 0.01734360938235813 0.2937765709409646 chr21 48129895 782456 0.01625717238734886 0.2819897073141409 chr22 51304566 563241 0.01097837958516207 0.22758067592446027 chrMT 16571 27555 1.6628447287429848 2.8864890202324744 chrX 155270560 3450176 0.022220413193589306 0.34665414180512466 chrY 59373566 166951 0.002811874226991857 0.10476525008064168