BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975291.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 51,826,716 number of mapped reads = 51,520,416 (99.41%) number of supplementary alignments = 112,851 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 25,843,669 number of mapped paired reads (second in pair) = 25,676,747 number of mapped paired reads (both in pair) = 51,276,706 number of mapped paired reads (singletons) = 243,710 number of mapped bases = 4,781,785,173 bp number of sequenced bases = 4,779,985,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,716,922 duplication rate = 57.99% >>>>>>> Insert size mean insert size = 145,311.3992 std insert size = 3,753,041.1451 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 55.9903 >>>>>>> ACTG content number of A's = 1,292,210,235 bp (27.03%) number of C's = 1,049,011,786 bp (21.95%) number of T's = 1,333,521,886 bp (27.9%) number of G's = 1,104,235,749 bp (23.1%) number of N's = 1,006,236 bp (0.02%) GC percentage = 45.05% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 41,255,341 number of insertions = 534,172 mapped reads with insertion percentage = 1.03% number of deletions = 1,232,890 mapped reads with deletion percentage = 2.36% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 1.5447X std coverageData = 22.8395X There is a 10.14% of reference with a coverageData >= 1X There is a 6.26% of reference with a coverageData >= 2X There is a 3.62% of reference with a coverageData >= 3X There is a 2.74% of reference with a coverageData >= 4X There is a 2.21% of reference with a coverageData >= 5X There is a 1.95% of reference with a coverageData >= 6X There is a 1.77% of reference with a coverageData >= 7X There is a 1.66% of reference with a coverageData >= 8X There is a 1.56% of reference with a coverageData >= 9X There is a 1.49% of reference with a coverageData >= 10X There is a 1.43% of reference with a coverageData >= 11X There is a 1.38% of reference with a coverageData >= 12X There is a 1.33% of reference with a coverageData >= 13X There is a 1.29% of reference with a coverageData >= 14X There is a 1.25% of reference with a coverageData >= 15X There is a 1.21% of reference with a coverageData >= 16X There is a 1.18% of reference with a coverageData >= 17X There is a 1.15% of reference with a coverageData >= 18X There is a 1.12% of reference with a coverageData >= 19X There is a 1.09% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 1.04% of reference with a coverageData >= 22X There is a 1.02% of reference with a coverageData >= 23X There is a 0.99% of reference with a coverageData >= 24X There is a 0.97% of reference with a coverageData >= 25X There is a 0.95% of reference with a coverageData >= 26X There is a 0.93% of reference with a coverageData >= 27X There is a 0.91% of reference with a coverageData >= 28X There is a 0.9% of reference with a coverageData >= 29X There is a 0.88% of reference with a coverageData >= 30X There is a 0.86% of reference with a coverageData >= 31X There is a 0.85% of reference with a coverageData >= 32X There is a 0.83% of reference with a coverageData >= 33X There is a 0.82% of reference with a coverageData >= 34X There is a 0.8% of reference with a coverageData >= 35X There is a 0.79% of reference with a coverageData >= 36X There is a 0.78% of reference with a coverageData >= 37X There is a 0.76% of reference with a coverageData >= 38X There is a 0.75% of reference with a coverageData >= 39X There is a 0.74% of reference with a coverageData >= 40X There is a 0.73% of reference with a coverageData >= 41X There is a 0.72% of reference with a coverageData >= 42X There is a 0.7% of reference with a coverageData >= 43X There is a 0.69% of reference with a coverageData >= 44X There is a 0.68% of reference with a coverageData >= 45X There is a 0.67% of reference with a coverageData >= 46X There is a 0.66% of reference with a coverageData >= 47X There is a 0.65% of reference with a coverageData >= 48X There is a 0.64% of reference with a coverageData >= 49X There is a 0.64% of reference with a coverageData >= 50X There is a 0.63% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 560212566 2.247587443322759 28.92174109210919 chr2 243199373 356286598 1.4649980121453685 19.72299225147557 chr3 198022430 318434497 1.6080728683109282 22.46993774541839 chr4 191154276 218487932 1.1429926474676402 17.764628748058932 chr5 180915260 233201457 1.2890093240338045 18.487119440515006 chr6 171115067 435395743 2.5444617509923892 37.39086260585253 chr7 159138663 252370260 1.5858513276563093 23.744459213379294 chr8 146364022 164895455 1.1266119415603377 16.96187893841367 chr9 141213431 198438871 1.4052407734502252 20.91746956750295 chr10 135534747 211080335 1.5573890804547708 22.57565352412183 chr11 135006516 214024526 1.5852903425787241 21.810623701853814 chr12 133851895 267603419 1.9992501338886535 25.07862663033196 chr13 115169878 107041809 0.9294253919414589 17.993212187240285 chr14 107349540 153487632 1.4297931039108318 22.4550620428934 chr15 102531392 171403481 1.6717170971403568 24.884805636330945 chr16 90354753 141750214 1.5688185656376041 21.031893017410123 chr17 81195210 172528003 2.1248544464630363 25.34120638416194 chr18 78077248 89913412 1.1515955582860706 17.988546062765028 chr19 59128983 161859531 2.737397512823787 33.42759444474581 chr20 63025520 113707880 1.8041561576961205 26.02223977318718 chr21 48129895 45600733 0.9474513293660832 15.299473719098781 chr22 51304566 67580544 1.3172422898967706 17.37753578887019 chrMT 16571 85370 5.151771166495685 10.092619902636795 chrX 155270560 117124833 0.7543273689487563 13.840793278417825 chrY 59373566 9270072 0.15613129923845234 3.9783807028162284