BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549076.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,529,104 number of mapped reads = 9,231,374 (87.67%) number of secondary alignments = 0 number of mapped bases = 366,428,016 bp number of sequenced bases = 366,390,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 341,459 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5427 >>>>>>> ACTG content number of A's = 108,564,997 bp (29.63%) number of C's = 74,299,065 bp (20.28%) number of T's = 110,514,442 bp (30.16%) number of G's = 72,926,926 bp (19.9%) number of N's = 85,178 bp (0.02%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,464,881 number of insertions = 9,167 mapped reads with insertion percentage = 0.1% number of deletions = 29,806 mapped reads with deletion percentage = 0.32% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.1184X std coverageData = 0.8068X There is a 9.81% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.26% 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 29689839 0.1191164093428678 1.848900398104021 chr2 243199373 32084814 0.1319280292716873 0.6795008632916196 chr3 198022430 25886044 0.13072278731252818 0.4242592826990538 chr4 191154276 25125098 0.1314388489012927 0.42649204343812114 chr5 180915260 23639784 0.13066771702950875 0.4283754598924776 chr6 171115067 22413399 0.13098436854774453 0.5568768038097383 chr7 159138663 20630093 0.12963595779361298 0.9121183206785535 chr8 146364022 19165278 0.1309425481625532 0.5508473720249017 chr9 141213431 15523295 0.10992789347353227 0.6598332738709575 chr10 135534747 17583916 0.12973732853907935 0.9005607693640949 chr11 135006516 17108245 0.1267216243103407 0.6699345273532223 chr12 133851895 16790880 0.12544372270560683 0.44032110897184007 chr13 115169878 12663341 0.10995358525950683 0.37425708250511464 chr14 107349540 11363651 0.1058565411644987 0.48448736446739193 chr15 102531392 10639165 0.10376495229870672 0.36907103481409803 chr16 90354753 9912748 0.10970920367631352 0.5137477747315082 chr17 81195210 8989477 0.1107143758849814 0.4632853764188232 chr18 78077248 10254834 0.13134215488742637 1.4618435590285337 chr19 59128983 6253680 0.10576336142970698 1.4828675805286997 chr20 63025520 7389710 0.11724948877851385 0.41762161016109456 chr21 48129895 4783867 0.09939491868827056 0.44693051568029685 chr22 51304566 3718499 0.07247890957697606 0.36129867290668005 chrMT 16571 9096 0.5489107476917506 1.1309501346426405 chrX 155270560 12125275 0.07809126855728478 0.4466480216401034 chrY 59373566 2683988 0.04520510019559883 0.3278815814755684