BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504422.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 139,801,286 number of mapped reads = 138,548,365 (99.1%) number of supplementary alignments = 2,297,695 (1.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 69,313,888 number of mapped paired reads (second in pair) = 69,234,477 number of mapped paired reads (both in pair) = 138,063,082 number of mapped paired reads (singletons) = 485,283 number of mapped bases = 13,250,818,411 bp number of sequenced bases = 13,246,834,492 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,150,861 duplication rate = 31.9% >>>>>>> Insert size mean insert size = 76,539.752 std insert size = 2,569,239.4778 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 52.8018 >>>>>>> ACTG content number of A's = 3,914,776,943 bp (29.55%) number of C's = 2,684,621,141 bp (20.27%) number of T's = 3,934,782,526 bp (29.7%) number of G's = 2,702,000,847 bp (20.4%) number of N's = 10,653,035 bp (0.08%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 74,439,402 number of insertions = 1,258,167 mapped reads with insertion percentage = 0.9% number of deletions = 2,522,765 mapped reads with deletion percentage = 1.8% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 4.2804X std coverageData = 168.3961X There is a 29.17% of reference with a coverageData >= 1X There is a 22.14% of reference with a coverageData >= 2X There is a 17.14% of reference with a coverageData >= 3X There is a 14.46% of reference with a coverageData >= 4X There is a 12.38% of reference with a coverageData >= 5X There is a 10.89% of reference with a coverageData >= 6X There is a 9.69% of reference with a coverageData >= 7X There is a 8.74% of reference with a coverageData >= 8X There is a 7.95% of reference with a coverageData >= 9X There is a 7.29% of reference with a coverageData >= 10X There is a 6.73% of reference with a coverageData >= 11X There is a 6.24% of reference with a coverageData >= 12X There is a 5.81% of reference with a coverageData >= 13X There is a 5.44% of reference with a coverageData >= 14X There is a 5.1% of reference with a coverageData >= 15X There is a 4.81% of reference with a coverageData >= 16X There is a 4.54% of reference with a coverageData >= 17X There is a 4.3% of reference with a coverageData >= 18X There is a 4.08% of reference with a coverageData >= 19X There is a 3.88% of reference with a coverageData >= 20X There is a 3.7% of reference with a coverageData >= 21X There is a 3.53% of reference with a coverageData >= 22X There is a 3.38% of reference with a coverageData >= 23X There is a 3.23% of reference with a coverageData >= 24X There is a 3.1% of reference with a coverageData >= 25X There is a 2.98% of reference with a coverageData >= 26X There is a 2.86% of reference with a coverageData >= 27X There is a 2.75% of reference with a coverageData >= 28X There is a 2.65% of reference with a coverageData >= 29X There is a 2.56% of reference with a coverageData >= 30X There is a 2.47% of reference with a coverageData >= 31X There is a 2.39% of reference with a coverageData >= 32X There is a 2.31% of reference with a coverageData >= 33X There is a 2.23% of reference with a coverageData >= 34X There is a 2.16% of reference with a coverageData >= 35X There is a 2.1% of reference with a coverageData >= 36X There is a 2.03% of reference with a coverageData >= 37X There is a 1.97% of reference with a coverageData >= 38X There is a 1.92% of reference with a coverageData >= 39X There is a 1.86% of reference with a coverageData >= 40X There is a 1.81% of reference with a coverageData >= 41X There is a 1.76% of reference with a coverageData >= 42X There is a 1.72% of reference with a coverageData >= 43X There is a 1.67% of reference with a coverageData >= 44X There is a 1.63% of reference with a coverageData >= 45X There is a 1.59% of reference with a coverageData >= 46X There is a 1.55% of reference with a coverageData >= 47X There is a 1.51% of reference with a coverageData >= 48X There is a 1.47% of reference with a coverageData >= 49X There is a 1.44% of reference with a coverageData >= 50X There is a 1.4% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 941071974 3.7756053333965416 34.46836890551028 chr2 243199373 985727716 4.053167176545311 22.74053648234077 chr3 198022430 953776366 4.816506726030985 36.058727686113265 chr4 191154276 779744739 4.079138355241397 34.92803471940184 chr5 180915260 868762021 4.802038374209008 31.79146861213742 chr6 171115067 789492364 4.613809747098425 40.3847627270545 chr7 159138663 679802166 4.2717599430881235 161.30841126392477 chr8 146364022 683551883 4.670217951512702 37.38079893631189 chr9 141213431 1310663633 9.281437493010138 708.3937494929779 chr10 135534747 891051413 6.574339294704996 272.93591119083675 chr11 135006516 588805396 4.361310945910196 27.281765360509212 chr12 133851895 529699582 3.957355867094747 20.604905791525688 chr13 115169878 324532351 2.817857903782793 17.788998694726647 chr14 107349540 348146096 3.243107478616117 21.031459870077118 chr15 102531392 293152007 2.8591439293050853 19.731430540851733 chr16 90354753 241407218 2.671771102069196 15.415190529598622 chr17 81195210 215969615 2.6598812294469094 16.83719038425476 chr18 78077248 319411052 4.090961966282419 32.36886491519018 chr19 59128983 154954218 2.6206136168450587 25.966435246227714 chr20 63025520 185841516 2.9486708876023555 18.014602700925238 chr21 48129895 144368425 2.9995582786956008 21.992204046534336 chr22 51304566 65089874 1.2686955387167684 8.82148046623896 chrMT 16571 5552 0.3350431476676121 1.339728934054283 chrX 155270560 945470268 6.089179223672536 62.26233721342093 chrY 59373566 10320966 0.17383099408245076 1.939226073462628