BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094092.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 346,268 number of mapped reads = 318,518 (91.99%) number of supplementary alignments = 25,831 (7.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 159,992 number of mapped paired reads (second in pair) = 158,526 number of mapped paired reads (both in pair) = 315,864 number of mapped paired reads (singletons) = 2,654 number of mapped bases = 39,827,869 bp number of sequenced bases = 39,066,553 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 297,668 duplication rate = 51.94% >>>>>>> Insert size mean insert size = 1,974,935.6971 std insert size = 12,252,018.3415 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 42.6768 >>>>>>> ACTG content number of A's = 11,267,749 bp (28.84%) number of C's = 8,322,695 bp (21.3%) number of T's = 10,656,278 bp (27.28%) number of G's = 8,819,355 bp (22.58%) number of N's = 476 bp (0%) GC percentage = 43.88% >>>>>>> Mismatches and indels general error rate = 0.0361 number of mismatches = 1,355,297 number of insertions = 26,375 mapped reads with insertion percentage = 8.13% number of deletions = 106,143 mapped reads with deletion percentage = 32.07% homopolymer indels = 28.4% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 2.2427X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 778644 0.0031239400603138316 1.0016461926359135 chr2 243199373 1727321 0.007102489528211078 1.9167259116609137 chr3 198022430 827786 0.004180263821628691 1.2398132846414263 chr4 191154276 1056791 0.005528471672796898 1.538378728990345 chr5 180915260 569760 0.003149319742292607 0.9875753217308881 chr6 171115067 942403 0.0055074226748250054 1.5613879885447277 chr7 159138663 993362 0.006242116034366834 1.5680947268872216 chr8 146364022 583153 0.003984264657608275 0.9409053099341301 chr9 141213431 643942 0.004560061995802651 2.0585351203621753 chr10 135534747 674649 0.004977682955353139 1.4079333641667697 chr11 135006516 1242182 0.009200904051179277 2.05900510418524 chr12 133851895 1185177 0.00885439089226193 2.1239967266952418 chr13 115169878 818992 0.00711116495234978 1.6284897326260845 chr14 107349540 174082 0.001621637130443223 0.5159070011493099 chr15 102531392 385619 0.0037609847333390342 0.778568693664322 chr16 90354753 187638 0.0020766810131172624 0.6266504491191256 chr17 81195210 300838 0.0037051200434114278 0.8875863045981811 chr18 78077248 234428 0.003002513613184727 0.8149252341673575 chr19 59128983 90712 0.0015341376664638388 0.4146834984222763 chr20 63025520 123706 0.0019627922149630817 0.5429884286584604 chr21 48129895 193531 0.004021014382017663 1.600125482299671 chr22 51304566 37921 7.391349923903459E-4 0.17832240251181705 chrMT 16571 119666 7.221410898557721 35.45186093749963 chrX 155270560 25306396 0.1629825769933463 7.823598913715137 chrY 59373566 629170 0.010596803297952493 2.178549682437215