BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506122.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 9,123,670 number of mapped reads = 6,636,621 (72.74%) number of supplementary alignments = 107,720 (1.18%) number of secondary alignments = 0 number of mapped bases = 529,111,816 bp number of sequenced bases = 528,891,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,583,516 duplication rate = 14.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6054 >>>>>>> ACTG content number of A's = 140,886,207 bp (26.64%) number of C's = 100,781,894 bp (19.06%) number of T's = 154,678,376 bp (29.25%) number of G's = 132,474,586 bp (25.05%) number of N's = 70,770 bp (0.01%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 4,392,601 number of insertions = 45,009 mapped reads with insertion percentage = 0.66% number of deletions = 105,561 mapped reads with deletion percentage = 1.56% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.1709X std coverageData = 1.3072X There is a 7.81% of reference with a coverageData >= 1X There is a 3.48% of reference with a coverageData >= 2X There is a 1.91% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.73% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% 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% 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 40194908 0.16126302048410945 2.4095160588466076 chr2 243199373 42949362 0.1766014503664037 1.3996401207642528 chr3 198022430 32430271 0.16377069506722042 0.7871150096031334 chr4 191154276 29762856 0.15570070742231265 1.2296928891618524 chr5 180915260 40420146 0.223420323968249 0.9886480759356631 chr6 171115067 19994085 0.11684584736188076 0.7518287410335237 chr7 159138663 27204737 0.17094989041098077 1.1895207199130458 chr8 146364022 31075059 0.21231350830192408 1.2725656082243346 chr9 141213431 14989001 0.10614430152893885 1.1287448377480112 chr10 135534747 30340331 0.223856477188097 1.6395528700432893 chr11 135006516 23048884 0.17072423378439008 1.2208512927060673 chr12 133851895 22617741 0.1689758744170189 0.8507858151511146 chr13 115169878 10969773 0.09524862915978777 0.6133204451765439 chr14 107349540 14038115 0.13077014582456525 0.819909523070357 chr15 102531392 20126687 0.1962978031157521 0.8985817356809237 chr16 90354753 20426549 0.22607055325578723 1.1811307553898982 chr17 81195210 14146537 0.17422871373816262 0.9846847854892228 chr18 78077248 10150236 0.13000248164484485 1.908568252122377 chr19 59128983 14085489 0.23821632447153707 1.8207305082594154 chr20 63025520 15184486 0.24092599315324967 1.1109214934341063 chr21 48129895 8032331 0.16688860426560248 1.1999716700561933 chr22 51304566 7034351 0.13710964829134312 0.862577555049996 chrMT 16571 161696 9.75776959748959 7.376064091759134 chrX 155270560 37565707 0.24193708710782005 1.0875592854891827 chrY 59373566 2162478 0.03642156174348699 1.393619303573576