BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504590.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 = 363,688,574 number of mapped reads = 347,718,484 (95.61%) number of supplementary alignments = 987,185 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 174,054,463 number of mapped paired reads (second in pair) = 173,664,021 number of mapped paired reads (both in pair) = 344,943,020 number of mapped paired reads (singletons) = 2,775,464 number of mapped bases = 33,402,182,008 bp number of sequenced bases = 33,391,464,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,408,158 duplication rate = 18.01% >>>>>>> Insert size mean insert size = 33,081.1596 std insert size = 1,723,007.3573 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.3731 >>>>>>> ACTG content number of A's = 9,488,271,772 bp (28.42%) number of C's = 7,162,295,392 bp (21.45%) number of T's = 9,393,272,106 bp (28.13%) number of G's = 7,340,564,168 bp (21.98%) number of N's = 7,061,436 bp (0.02%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 187,017,767 number of insertions = 3,372,155 mapped reads with insertion percentage = 0.93% number of deletions = 4,147,652 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.41% >>>>>>> Coverage mean coverageData = 10.7899X std coverageData = 94.9609X There is a 90.87% of reference with a coverageData >= 1X There is a 89.11% of reference with a coverageData >= 2X There is a 86.1% of reference with a coverageData >= 3X There is a 81.92% of reference with a coverageData >= 4X There is a 76.69% of reference with a coverageData >= 5X There is a 70.73% of reference with a coverageData >= 6X There is a 64.31% of reference with a coverageData >= 7X There is a 57.73% of reference with a coverageData >= 8X There is a 51.25% of reference with a coverageData >= 9X There is a 45.05% of reference with a coverageData >= 10X There is a 39.28% of reference with a coverageData >= 11X There is a 34% of reference with a coverageData >= 12X There is a 29.27% of reference with a coverageData >= 13X There is a 25.09% of reference with a coverageData >= 14X There is a 21.44% of reference with a coverageData >= 15X There is a 18.28% of reference with a coverageData >= 16X There is a 15.59% of reference with a coverageData >= 17X There is a 13.29% of reference with a coverageData >= 18X There is a 11.36% of reference with a coverageData >= 19X There is a 9.73% of reference with a coverageData >= 20X There is a 8.36% of reference with a coverageData >= 21X There is a 7.22% of reference with a coverageData >= 22X There is a 6.26% of reference with a coverageData >= 23X There is a 5.46% of reference with a coverageData >= 24X There is a 4.79% of reference with a coverageData >= 25X There is a 4.23% of reference with a coverageData >= 26X There is a 3.76% of reference with a coverageData >= 27X There is a 3.36% of reference with a coverageData >= 28X There is a 3.02% of reference with a coverageData >= 29X There is a 2.73% of reference with a coverageData >= 30X There is a 2.49% of reference with a coverageData >= 31X There is a 2.28% of reference with a coverageData >= 32X There is a 2.1% of reference with a coverageData >= 33X There is a 1.94% of reference with a coverageData >= 34X There is a 1.8% of reference with a coverageData >= 35X There is a 1.68% of reference with a coverageData >= 36X There is a 1.57% of reference with a coverageData >= 37X There is a 1.48% of reference with a coverageData >= 38X There is a 1.39% of reference with a coverageData >= 39X There is a 1.31% of reference with a coverageData >= 40X There is a 1.24% of reference with a coverageData >= 41X There is a 1.18% of reference with a coverageData >= 42X There is a 1.12% of reference with a coverageData >= 43X There is a 1.07% of reference with a coverageData >= 44X There is a 1.02% of reference with a coverageData >= 45X There is a 0.98% of reference with a coverageData >= 46X There is a 0.93% of reference with a coverageData >= 47X There is a 0.9% of reference with a coverageData >= 48X There is a 0.86% of reference with a coverageData >= 49X There is a 0.83% of reference with a coverageData >= 50X There is a 0.79% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3104872351 12.456828948081137 172.10161496534613 chr2 243199373 2359596988 9.702315260492057 57.35468466420613 chr3 198022430 1975854377 9.97793218172305 16.527033531481354 chr4 191154276 1893796907 9.907164760468136 113.80210758708776 chr5 180915260 1577315545 8.718532339394697 10.361429416066128 chr6 171115067 1565242831 9.147311563160011 22.453604177680713 chr7 159138663 2816941083 17.70117349169887 136.7559275950618 chr8 146364022 2936509401 20.063054846907665 66.96047548223623 chr9 141213431 1203856182 8.525082730976205 60.38669050541563 chr10 135534747 1625964934 11.996664840492896 257.3845353922931 chr11 135006516 1435268221 10.631103323931416 38.708744777620865 chr12 133851895 1248641291 9.328529050709369 8.74711184633951 chr13 115169878 811314860 7.044505682293074 6.393296883536853 chr14 107349540 1083472702 10.092942196119331 9.44487140436135 chr15 102531392 872430828 8.508914304021152 7.173084375051858 chr16 90354753 927726120 10.267596215995411 73.3474146208035 chr17 81195210 1035731934 12.75607186680101 44.6978030487449 chr18 78077248 569599566 7.295333539419832 93.94804112187305 chr19 59128983 667398928 11.287170760234453 89.43366971479627 chr20 63025520 1404389301 22.282867336913682 29.066134206624078 chr21 48129895 401161640 8.334978499329782 40.60562774734245 chr22 51304566 450069775 8.772509156397502 9.438477397759677 chrMT 16571 119702612 7223.620300525014 1539.469066680494 chrX 155270560 1187200676 7.646012714837894 18.61203659410907 chrY 59373566 128122955 2.1579124117288155 115.69343624590857