BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618575.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 = 59,683,086 number of mapped reads = 57,711,914 (96.7%) number of supplementary alignments = 73,726 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,110,037 number of mapped paired reads (second in pair) = 28,601,877 number of mapped paired reads (both in pair) = 56,725,008 number of mapped paired reads (singletons) = 986,906 number of mapped bases = 5,533,146,507 bp number of sequenced bases = 5,529,618,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,085,375 duplication rate = 18.65% >>>>>>> Insert size mean insert size = 23,352.5772 std insert size = 1,501,967.416 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 54.0236 >>>>>>> ACTG content number of A's = 1,480,973,164 bp (26.78%) number of C's = 1,259,991,681 bp (22.79%) number of T's = 1,485,530,240 bp (26.86%) number of G's = 1,302,894,566 bp (23.56%) number of N's = 229,021 bp (0%) GC percentage = 46.35% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 70,154,562 number of insertions = 982,696 mapped reads with insertion percentage = 1.67% number of deletions = 2,545,246 mapped reads with deletion percentage = 4.31% homopolymer indels = 52.13% >>>>>>> Coverage mean coverageData = 1.7874X std coverageData = 7.7386X There is a 27.22% of reference with a coverageData >= 1X There is a 19.38% of reference with a coverageData >= 2X There is a 14.84% of reference with a coverageData >= 3X There is a 11.94% of reference with a coverageData >= 4X There is a 9.86% of reference with a coverageData >= 5X There is a 8.33% of reference with a coverageData >= 6X There is a 7.15% of reference with a coverageData >= 7X There is a 6.21% of reference with a coverageData >= 8X There is a 5.45% of reference with a coverageData >= 9X There is a 4.82% of reference with a coverageData >= 10X There is a 4.29% of reference with a coverageData >= 11X There is a 3.85% of reference with a coverageData >= 12X There is a 3.47% of reference with a coverageData >= 13X There is a 3.14% of reference with a coverageData >= 14X There is a 2.86% of reference with a coverageData >= 15X There is a 2.61% of reference with a coverageData >= 16X There is a 2.39% of reference with a coverageData >= 17X There is a 2.2% of reference with a coverageData >= 18X There is a 2.03% of reference with a coverageData >= 19X There is a 1.87% of reference with a coverageData >= 20X There is a 1.74% of reference with a coverageData >= 21X There is a 1.61% of reference with a coverageData >= 22X There is a 1.5% of reference with a coverageData >= 23X There is a 1.4% of reference with a coverageData >= 24X There is a 1.3% of reference with a coverageData >= 25X There is a 1.22% of reference with a coverageData >= 26X There is a 1.14% of reference with a coverageData >= 27X There is a 1.07% of reference with a coverageData >= 28X There is a 1.01% of reference with a coverageData >= 29X There is a 0.95% of reference with a coverageData >= 30X There is a 0.89% of reference with a coverageData >= 31X There is a 0.84% of reference with a coverageData >= 32X There is a 0.8% of reference with a coverageData >= 33X There is a 0.75% of reference with a coverageData >= 34X There is a 0.71% of reference with a coverageData >= 35X There is a 0.67% of reference with a coverageData >= 36X There is a 0.64% of reference with a coverageData >= 37X There is a 0.61% of reference with a coverageData >= 38X There is a 0.58% of reference with a coverageData >= 39X There is a 0.55% of reference with a coverageData >= 40X There is a 0.52% of reference with a coverageData >= 41X There is a 0.5% of reference with a coverageData >= 42X There is a 0.47% of reference with a coverageData >= 43X There is a 0.45% of reference with a coverageData >= 44X There is a 0.43% of reference with a coverageData >= 45X There is a 0.41% of reference with a coverageData >= 46X There is a 0.39% of reference with a coverageData >= 47X There is a 0.37% of reference with a coverageData >= 48X There is a 0.36% of reference with a coverageData >= 49X There is a 0.34% of reference with a coverageData >= 50X There is a 0.33% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 509360003 2.0435656326810117 8.366574965869269 chr2 243199373 457500376 1.8811741591126552 9.251733447538259 chr3 198022430 333871996 1.686031203636881 5.998967018347581 chr4 191154276 241025162 1.2608933843572507 5.543355344834438 chr5 180915260 292483670 1.616688774622992 5.77448511376662 chr6 171115067 276563259 1.616241420751102 5.988867953857602 chr7 159138663 265353381 1.6674350280296122 6.035326850450665 chr8 146364022 260768518 1.7816435653838483 6.309235398192391 chr9 141213431 239120230 1.6933249784151196 7.276792242933825 chr10 135534747 283576487 2.092278867794692 7.3419565013617385 chr11 135006516 288702800 2.1384360440795316 7.912195254606839 chr12 133851895 248164106 1.8540201167865422 6.934781131345928 chr13 115169878 131265523 1.1397556833393536 4.782249367048796 chr14 107349540 176025403 1.6397406360567544 6.492538130497394 chr15 102531392 193504523 1.8872710028163862 7.1841764123771545 chr16 90354753 213521638 2.3631478246639666 18.092891224762703 chr17 81195210 200847154 2.473633038205086 8.862456408039963 chr18 78077248 140487504 1.7993398537817316 7.278620431863549 chr19 59128983 148470777 2.5109644960407995 9.56256285576022 chr20 63025520 171871850 2.7270199436672637 9.247611600376263 chr21 48129895 70876223 1.4726029009620736 10.075819137455147 chr22 51304566 114246407 2.2268272769328172 8.885286285176873 chrMT 16571 2558 0.1543660611912377 0.7127862129364534 chrX 155270560 267464633 1.7225714456108099 6.045739751024133 chrY 59373566 8072326 0.135958247816882 6.09641324000128