BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961012.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 = 388,735,092 number of mapped reads = 370,886,089 (95.41%) number of supplementary alignments = 6,296,520 (1.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 192,072,014 number of mapped paired reads (second in pair) = 178,814,075 number of mapped paired reads (both in pair) = 356,732,772 number of mapped paired reads (singletons) = 14,153,317 number of mapped bases = 36,286,275,143 bp number of sequenced bases = 36,275,616,424 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,613,810 duplication rate = 11.08% >>>>>>> Insert size mean insert size = 86,318.0374 std insert size = 2,825,874.4224 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 53.0883 >>>>>>> ACTG content number of A's = 10,604,384,777 bp (29.23%) number of C's = 7,505,668,615 bp (20.69%) number of T's = 10,557,492,170 bp (29.1%) number of G's = 7,567,246,159 bp (20.86%) number of N's = 40,824,703 bp (0.11%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 399,077,309 number of insertions = 3,735,803 mapped reads with insertion percentage = 0.97% number of deletions = 4,373,621 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.55% >>>>>>> Coverage mean coverageData = 11.7215X std coverageData = 145.2783X There is a 91.29% of reference with a coverageData >= 1X There is a 90.44% of reference with a coverageData >= 2X There is a 88.88% of reference with a coverageData >= 3X There is a 86.53% of reference with a coverageData >= 4X There is a 83.26% of reference with a coverageData >= 5X There is a 79.11% of reference with a coverageData >= 6X There is a 74.17% of reference with a coverageData >= 7X There is a 68.61% of reference with a coverageData >= 8X There is a 62.61% of reference with a coverageData >= 9X There is a 56.4% of reference with a coverageData >= 10X There is a 50.17% of reference with a coverageData >= 11X There is a 44.1% of reference with a coverageData >= 12X There is a 38.34% of reference with a coverageData >= 13X There is a 32.99% of reference with a coverageData >= 14X There is a 28.1% of reference with a coverageData >= 15X There is a 23.73% of reference with a coverageData >= 16X There is a 19.88% of reference with a coverageData >= 17X There is a 16.53% of reference with a coverageData >= 18X There is a 13.66% of reference with a coverageData >= 19X There is a 11.23% of reference with a coverageData >= 20X There is a 9.19% of reference with a coverageData >= 21X There is a 7.5% of reference with a coverageData >= 22X There is a 6.1% of reference with a coverageData >= 23X There is a 4.96% of reference with a coverageData >= 24X There is a 4.02% of reference with a coverageData >= 25X There is a 3.27% of reference with a coverageData >= 26X There is a 2.66% of reference with a coverageData >= 27X There is a 2.17% of reference with a coverageData >= 28X There is a 1.78% of reference with a coverageData >= 29X There is a 1.47% of reference with a coverageData >= 30X There is a 1.21% of reference with a coverageData >= 31X There is a 1.01% of reference with a coverageData >= 32X There is a 0.85% of reference with a coverageData >= 33X There is a 0.72% of reference with a coverageData >= 34X There is a 0.62% of reference with a coverageData >= 35X There is a 0.53% of reference with a coverageData >= 36X There is a 0.46% of reference with a coverageData >= 37X There is a 0.41% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.33% of reference with a coverageData >= 40X There is a 0.3% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.25% of reference with a coverageData >= 43X There is a 0.24% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3355809748 13.463596337439014 369.1041493525009 chr2 243199373 3066789254 12.61018569320078 86.43044203700974 chr3 198022430 2457772961 12.411588732650134 32.16176225079312 chr4 191154276 2172985483 11.36770533451211 98.705104234749 chr5 180915260 1744683438 9.643649949705734 14.477101482991328 chr6 171115067 1781745715 10.412558906925478 45.00146681132224 chr7 159138663 2048881235 12.87481744772482 91.83817954541422 chr8 146364022 1866121439 12.7498644373137 128.37867986191836 chr9 141213431 1727804704 12.235413386422145 112.71521659628598 chr10 135534747 1801454171 13.291456330382939 321.1413598789057 chr11 135006516 1644537687 12.181172699842133 61.72553676926166 chr12 133851895 1361473111 10.171489249367744 12.295389569119287 chr13 115169878 1110639016 9.64348521754968 7.157510767972508 chr14 107349540 797653654 7.430433833251637 11.831578866635443 chr15 102531392 957315836 9.33680717023719 7.216500486054649 chr16 90354753 1351048862 14.952714905877723 150.99802941483514 chr17 81195210 772530544 9.514484216495037 37.044089646976474 chr18 78077248 1381446013 17.6933235787204 141.72520160387464 chr19 59128983 800858701 13.544266455589131 180.5426361752347 chr20 63025520 706375173 11.20776429928702 35.73176636992681 chr21 48129895 508908678 10.57365028533721 53.93332642134766 chr22 51304566 417265282 8.133102266180362 9.524693691652486 chrMT 16571 8163943 492.6644740812262 88.54449166769066 chrX 155270560 2318030265 14.928974719998434 47.59203839919655 chrY 59373566 125980230 2.121823540125584 112.95642473063758