BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153344.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 = 63,201,886 number of mapped reads = 62,415,556 (98.76%) number of supplementary alignments = 432,109 (0.68%) number of secondary alignments = 0 number of mapped bases = 6,209,349,407 bp number of sequenced bases = 6,208,500,183 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,480,591 duplication rate = 34.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0021 >>>>>>> ACTG content number of A's = 1,643,025,406 bp (26.46%) number of C's = 1,457,297,464 bp (23.47%) number of T's = 1,644,392,640 bp (26.49%) number of G's = 1,463,497,993 bp (23.57%) number of N's = 286,680 bp (0%) GC percentage = 47.05% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 18,680,782 number of insertions = 546,913 mapped reads with insertion percentage = 0.87% number of deletions = 389,760 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 2.0058X std coverageData = 19.9574X There is a 11.73% of reference with a coverageData >= 1X There is a 6.85% of reference with a coverageData >= 2X There is a 5.46% of reference with a coverageData >= 3X There is a 4.85% of reference with a coverageData >= 4X There is a 4.45% of reference with a coverageData >= 5X There is a 4.14% of reference with a coverageData >= 6X There is a 3.89% of reference with a coverageData >= 7X There is a 3.68% of reference with a coverageData >= 8X There is a 3.49% of reference with a coverageData >= 9X There is a 3.32% of reference with a coverageData >= 10X There is a 3.18% of reference with a coverageData >= 11X There is a 3.04% of reference with a coverageData >= 12X There is a 2.92% of reference with a coverageData >= 13X There is a 2.8% of reference with a coverageData >= 14X There is a 2.7% of reference with a coverageData >= 15X There is a 2.6% of reference with a coverageData >= 16X There is a 2.5% of reference with a coverageData >= 17X There is a 2.42% of reference with a coverageData >= 18X There is a 2.33% of reference with a coverageData >= 19X There is a 2.26% of reference with a coverageData >= 20X There is a 2.18% of reference with a coverageData >= 21X There is a 2.11% of reference with a coverageData >= 22X There is a 2.05% of reference with a coverageData >= 23X There is a 1.99% of reference with a coverageData >= 24X There is a 1.93% of reference with a coverageData >= 25X There is a 1.87% of reference with a coverageData >= 26X There is a 1.81% of reference with a coverageData >= 27X There is a 1.76% of reference with a coverageData >= 28X There is a 1.71% of reference with a coverageData >= 29X There is a 1.67% of reference with a coverageData >= 30X There is a 1.62% of reference with a coverageData >= 31X There is a 1.58% of reference with a coverageData >= 32X There is a 1.53% of reference with a coverageData >= 33X There is a 1.49% of reference with a coverageData >= 34X There is a 1.46% of reference with a coverageData >= 35X There is a 1.42% of reference with a coverageData >= 36X There is a 1.38% of reference with a coverageData >= 37X There is a 1.35% of reference with a coverageData >= 38X There is a 1.32% of reference with a coverageData >= 39X There is a 1.28% of reference with a coverageData >= 40X There is a 1.25% of reference with a coverageData >= 41X There is a 1.22% of reference with a coverageData >= 42X There is a 1.19% of reference with a coverageData >= 43X There is a 1.17% of reference with a coverageData >= 44X There is a 1.14% of reference with a coverageData >= 45X There is a 1.11% of reference with a coverageData >= 46X There is a 1.09% of reference with a coverageData >= 47X There is a 1.06% of reference with a coverageData >= 48X There is a 1.04% of reference with a coverageData >= 49X There is a 1.02% of reference with a coverageData >= 50X There is a 1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 673350892 2.701501361555284 23.719424755208408 chr2 243199373 406683803 1.672223895906179 13.826873119793355 chr3 198022430 277400313 1.4008529892295534 12.026689832806605 chr4 191154276 225024923 1.1771901089986603 12.116839747941183 chr5 180915260 332826748 1.8396831090975962 24.08785876169784 chr6 171115067 300171224 1.7542068577748329 14.33315179379037 chr7 159138663 335648899 2.109159978301439 22.092120346076353 chr8 146364022 374347051 2.557643920170491 44.50688325551406 chr9 141213431 191580810 1.3566755558824997 12.301061071710846 chr10 135534747 285491079 2.106405075592903 16.398263885446415 chr11 135006516 312285252 2.3131124426616565 16.230796117209135 chr12 133851895 300033378 2.2415325386315974 16.12774949244022 chr13 115169878 83912144 0.7285945375404496 7.507203123525132 chr14 107349540 157507517 1.467239794413651 12.293039820507254 chr15 102531392 321960000 3.1401114694707353 27.11038014319775 chr16 90354753 264962665 2.9324706913868717 22.157511820477012 chr17 81195210 230333615 2.8367882169403837 17.075060233753458 chr18 78077248 67992199 0.8708324222698013 8.884128628146877 chr19 59128983 353708049 5.981974169926109 31.780395771123704 chr20 63025520 151592420 2.4052545698948617 17.72686538548315 chr21 48129895 69242201 1.4386526502914665 17.56179486622688 chr22 51304566 95311285 1.8577544345663113 14.909047601992425 chrMT 16571 2035 0.12280490012672741 0.37312822368166354 chrX 155270560 390698703 2.5162445669030884 21.473111061191307 chrY 59373566 7282202 0.12265057483662005 5.394057646469332