BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506315.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 = 9,889,590 number of mapped reads = 7,237,427 (73.18%) number of supplementary alignments = 116,627 (1.18%) number of secondary alignments = 0 number of mapped bases = 575,424,704 bp number of sequenced bases = 575,160,036 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,462,154 duplication rate = 14.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5107 >>>>>>> ACTG content number of A's = 166,536,237 bp (28.95%) number of C's = 102,423,192 bp (17.81%) number of T's = 161,127,666 bp (28.01%) number of G's = 144,976,871 bp (25.21%) number of N's = 96,070 bp (0.02%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 4,929,041 number of insertions = 53,003 mapped reads with insertion percentage = 0.71% number of deletions = 128,439 mapped reads with deletion percentage = 1.74% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.1859X std coverageData = 1.2386X There is a 9.6% of reference with a coverageData >= 1X There is a 4.02% of reference with a coverageData >= 2X There is a 1.94% of reference with a coverageData >= 3X There is a 1.03% of reference with a coverageData >= 4X There is a 0.59% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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% 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 43663608 0.17517953546041518 1.8241617519593716 chr2 243199373 45438844 0.18683783366497414 1.2374385040443134 chr3 198022430 36494210 0.1842933146512746 0.7469333652045456 chr4 191154276 36174067 0.18924016640883304 1.312967826028697 chr5 180915260 43731786 0.24172524749985158 0.8844368816600413 chr6 171115067 21098546 0.12330034034933932 0.6532902635902263 chr7 159138663 29549290 0.18568265839961218 1.134067107494772 chr8 146364022 37640445 0.25717006464881104 2.437132501299216 chr9 141213431 15016991 0.10634251213682358 0.9527633092682899 chr10 135534747 33223569 0.24512953124854397 1.6207788874961482 chr11 135006516 24127597 0.1787143147964799 1.0783749232929278 chr12 133851895 25338832 0.18930499265624892 0.7835289043695347 chr13 115169878 11236715 0.09756644007211678 0.5366223315052094 chr14 107349540 17594746 0.16390145686697866 0.7715976973210826 chr15 102531392 21525408 0.20993968364342502 0.8213893577985004 chr16 90354753 19181816 0.2122944877066954 1.1238786688283533 chr17 81195210 14578387 0.17954737724060324 0.8690067035643825 chr18 78077248 10320908 0.13218841934592776 1.5805284677023752 chr19 59128983 13629604 0.23050631532086388 1.46007602916634 chr20 63025520 15636112 0.24809175711679968 0.9792627159243972 chr21 48129895 9932421 0.2063669783613698 1.0895983034501266 chr22 51304566 6702643 0.13064418087076304 0.6536056289236056 chrMT 16571 55034 3.321103131977551 3.9846309842748417 chrX 155270560 41098064 0.2646867764243267 0.9974971335436292 chrY 59373566 2435061 0.041012544201909654 1.4861131042743352