BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080707.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 = 2,092,222 number of mapped reads = 1,898,411 (90.74%) number of supplementary alignments = 10,902 (0.52%) number of secondary alignments = 0 number of mapped bases = 128,155,843 bp number of sequenced bases = 128,109,403 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,031 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2884 >>>>>>> ACTG content number of A's = 35,727,098 bp (27.89%) number of C's = 23,577,115 bp (18.4%) number of T's = 40,905,622 bp (31.93%) number of G's = 27,897,681 bp (21.78%) number of N's = 1,887 bp (0%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,031,365 number of insertions = 9,163 mapped reads with insertion percentage = 0.48% number of deletions = 26,323 mapped reads with deletion percentage = 1.37% homopolymer indels = 48.2% >>>>>>> Coverage mean coverageData = 0.0414X std coverageData = 0.3651X There is a 3.45% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% 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 15255234 0.06120439715975672 0.5290165175493134 chr2 243199373 8484017 0.03488502826033191 0.3595460041377949 chr3 198022430 7859572 0.039690311850026284 0.2285659595618032 chr4 191154276 6163420 0.03224317095579907 0.21451192398471666 chr5 180915260 5880377 0.032503488097134534 0.2064249162724943 chr6 171115067 7548246 0.04411210615369131 0.3263598526414309 chr7 159138663 8189748 0.05146296849308078 0.9038977133893962 chr8 146364022 15217367 0.10396931426221671 0.49606283079838087 chr9 141213431 4033393 0.028562389366490217 0.2656999658087511 chr10 135534747 6105659 0.045048661949396634 0.31466089573075323 chr11 135006516 5296277 0.03922978799038115 0.26342438528490136 chr12 133851895 4073073 0.030429699930658433 0.2022013702500978 chr13 115169878 2702270 0.023463339954219627 0.17645355934382043 chr14 107349540 2461440 0.022929208639366316 0.1804142659063178 chr15 102531392 2280824 0.022245128594372346 0.16956789625510998 chr16 90354753 3164108 0.03501872225803108 0.22966555311319523 chr17 81195210 2047428 0.02521611804440188 0.19239923571029577 chr18 78077248 4118128 0.05274427705238791 0.42005774154451025 chr19 59128983 2126520 0.035964088880067496 0.3404766838854899 chr20 63025520 3255384 0.05165183881069129 0.26752105564657336 chr21 48129895 1913105 0.03974878814923656 0.24303375086968296 chr22 51304566 1189476 0.023184603101408168 0.17332601622933838 chrMT 16571 20252 1.2221350552169452 1.3192177234017368 chrX 155270560 8491600 0.05468905373948545 0.2891140598755127 chrY 59373566 278925 0.004697797669757616 0.1002534723560374