BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506316.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 = 5,818,804 number of mapped reads = 4,121,184 (70.83%) number of supplementary alignments = 77,570 (1.33%) number of secondary alignments = 0 number of mapped bases = 319,347,804 bp number of sequenced bases = 319,199,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 539,696 duplication rate = 9.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8584 >>>>>>> ACTG content number of A's = 88,108,617 bp (27.6%) number of C's = 57,322,991 bp (17.96%) number of T's = 89,813,168 bp (28.14%) number of G's = 83,887,437 bp (26.28%) number of N's = 67,249 bp (0.02%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 2,429,650 number of insertions = 29,661 mapped reads with insertion percentage = 0.7% number of deletions = 70,235 mapped reads with deletion percentage = 1.67% homopolymer indels = 41.92% >>>>>>> Coverage mean coverageData = 0.1032X std coverageData = 0.7482X There is a 7.02% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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% 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 23402557 0.09389166978243958 1.0879014765145318 chr2 243199373 25629936 0.10538652169962626 0.8199711190811757 chr3 198022430 19197634 0.09694676507100736 0.44174937724791813 chr4 191154276 20350367 0.10646043303786727 0.8599009842512308 chr5 180915260 23627487 0.1305997459805215 0.5288186998607219 chr6 171115067 11429405 0.0667936798341668 0.39054524731761014 chr7 159138663 16307994 0.10247663071041385 0.7274906004117567 chr8 146364022 20151106 0.13767800122355206 1.109724611513512 chr9 141213431 8995560 0.06370187266393945 0.5508692764697465 chr10 135534747 18803421 0.13873505810284945 1.1547316120197846 chr11 135006516 13842722 0.10253373251999184 0.6346194053736655 chr12 133851895 13729348 0.102571188850184 0.4750145503417719 chr13 115169878 6340892 0.05505686130882243 0.3350291948459623 chr14 107349540 9324926 0.08686507645957309 0.4632146173895966 chr15 102531392 11379828 0.11098872041062312 0.4911565360598523 chr16 90354753 12113061 0.1340611378794871 0.7656221432922713 chr17 81195210 8613274 0.10608106069311231 0.5451192909960201 chr18 78077248 5485154 0.07025291157803103 0.8527975363474046 chr19 59128983 8511762 0.1439524505266732 0.8905508013531848 chr20 63025520 8662808 0.1374492110497462 0.6073825162250297 chr21 48129895 5407663 0.11235559520751084 0.744247806560731 chr22 51304566 3997689 0.07792072541847445 0.424506786680848 chrMT 16571 14303 0.8631343914066744 1.5034070105796666 chrX 155270560 22466745 0.1446941712582218 0.6014717973481027 chrY 59373566 1562162 0.026310732287833274 1.2044107466368756