BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618650.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 68,781,667 number of mapped reads = 64,108,771 (93.21%) number of supplementary alignments = 135,912 (0.2%) number of secondary alignments = 0 number of mapped bases = 6,114,342,325 bp number of sequenced bases = 6,110,470,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,506,614 duplication rate = 39.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.5092 >>>>>>> ACTG content number of A's = 1,566,427,145 bp (25.64%) number of C's = 1,488,999,230 bp (24.37%) number of T's = 1,791,463,261 bp (29.32%) number of G's = 1,261,081,521 bp (20.64%) number of N's = 2,498,884 bp (0.04%) GC percentage = 45.01% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 76,373,124 number of insertions = 1,150,009 mapped reads with insertion percentage = 1.77% number of deletions = 2,717,696 mapped reads with deletion percentage = 4.14% homopolymer indels = 50.29% >>>>>>> Coverage mean coverageData = 1.9751X std coverageData = 54.0016X There is a 17.61% of reference with a coverageData >= 1X There is a 11.29% of reference with a coverageData >= 2X There is a 8.31% of reference with a coverageData >= 3X There is a 6.5% of reference with a coverageData >= 4X There is a 5.28% of reference with a coverageData >= 5X There is a 4.41% of reference with a coverageData >= 6X There is a 3.76% of reference with a coverageData >= 7X There is a 3.26% of reference with a coverageData >= 8X There is a 2.87% of reference with a coverageData >= 9X There is a 2.55% of reference with a coverageData >= 10X There is a 2.29% of reference with a coverageData >= 11X There is a 2.08% of reference with a coverageData >= 12X There is a 1.9% of reference with a coverageData >= 13X There is a 1.75% of reference with a coverageData >= 14X There is a 1.62% of reference with a coverageData >= 15X There is a 1.5% of reference with a coverageData >= 16X There is a 1.4% of reference with a coverageData >= 17X There is a 1.31% of reference with a coverageData >= 18X There is a 1.23% of reference with a coverageData >= 19X There is a 1.16% of reference with a coverageData >= 20X There is a 1.1% of reference with a coverageData >= 21X There is a 1.04% of reference with a coverageData >= 22X There is a 0.99% of reference with a coverageData >= 23X There is a 0.95% of reference with a coverageData >= 24X There is a 0.9% of reference with a coverageData >= 25X There is a 0.87% of reference with a coverageData >= 26X There is a 0.83% of reference with a coverageData >= 27X There is a 0.8% of reference with a coverageData >= 28X There is a 0.77% of reference with a coverageData >= 29X There is a 0.74% of reference with a coverageData >= 30X There is a 0.71% of reference with a coverageData >= 31X There is a 0.69% of reference with a coverageData >= 32X There is a 0.67% of reference with a coverageData >= 33X There is a 0.64% of reference with a coverageData >= 34X There is a 0.62% of reference with a coverageData >= 35X There is a 0.61% of reference with a coverageData >= 36X There is a 0.59% of reference with a coverageData >= 37X There is a 0.57% of reference with a coverageData >= 38X There is a 0.56% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.53% of reference with a coverageData >= 41X There is a 0.51% of reference with a coverageData >= 42X There is a 0.5% of reference with a coverageData >= 43X There is a 0.49% of reference with a coverageData >= 44X There is a 0.48% of reference with a coverageData >= 45X There is a 0.47% of reference with a coverageData >= 46X There is a 0.46% of reference with a coverageData >= 47X There is a 0.45% of reference with a coverageData >= 48X There is a 0.44% of reference with a coverageData >= 49X There is a 0.43% of reference with a coverageData >= 50X There is a 0.42% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 610801900 2.4505531723429486 67.70212932681666 chr2 243199373 516985222 2.125767084111685 64.34819163757886 chr3 198022430 398858701 2.014209708465854 48.39010125618662 chr4 191154276 280126148 1.4654453662339209 34.12246571800988 chr5 180915260 368013983 2.034178780717558 56.41492455066235 chr6 171115067 316989203 1.8524914758090822 36.4292621540134 chr7 159138663 328981260 2.0672616810912885 65.90044168371473 chr8 146364022 327084147 2.234730520045425 58.9647412780063 chr9 141213431 252116307 1.7853564297294073 41.21802734150383 chr10 135534747 328393959 2.422950322842304 55.6754289358782 chr11 135006516 328882716 2.4360506866201925 60.92798774220023 chr12 133851895 289703899 2.164361580387039 57.72530866888951 chr13 115169878 182452453 1.5842028850634018 59.21141339462352 chr14 107349540 172140783 1.6035539882145746 37.05465887934565 chr15 102531392 217007703 2.116500115398804 56.92105737320726 chr16 90354753 208872260 2.311690896880654 58.01531696267867 chr17 81195210 242652554 2.9885082383554398 73.61255582346048 chr18 78077248 164823296 2.1110285034636465 49.8313352876978 chr19 59128983 142186627 2.404685820488406 56.88669758256061 chr20 63025520 188833116 2.9961373741938186 66.68285306167867 chr21 48129895 72670951 1.5098921574626332 44.11352599518898 chr22 51304566 114300989 2.2278911588492925 46.33496921930814 chrMT 16571 7182 0.4334077605455314 1.5833058130523838 chrX 155270560 12775585 0.08227950617296673 11.266548958149224 chrY 59373566 48681381 0.8199167454419025 32.89051789959463