BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618652.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 = 54,769,551 number of mapped reads = 53,102,546 (96.96%) number of supplementary alignments = 120,905 (0.22%) number of secondary alignments = 0 number of mapped bases = 5,207,904,921 bp number of sequenced bases = 5,203,535,086 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,983,634 duplication rate = 33.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.9176 >>>>>>> ACTG content number of A's = 1,355,119,443 bp (26.04%) number of C's = 1,239,558,514 bp (23.82%) number of T's = 1,388,389,872 bp (26.68%) number of G's = 1,219,562,540 bp (23.44%) number of N's = 904,717 bp (0.02%) GC percentage = 47.26% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 44,504,462 number of insertions = 859,003 mapped reads with insertion percentage = 1.59% number of deletions = 2,289,005 mapped reads with deletion percentage = 4.22% homopolymer indels = 51.2% >>>>>>> Coverage mean coverageData = 1.6823X std coverageData = 34.7484X There is a 19.42% of reference with a coverageData >= 1X There is a 13.91% of reference with a coverageData >= 2X There is a 10.95% of reference with a coverageData >= 3X There is a 9.01% of reference with a coverageData >= 4X There is a 7.62% of reference with a coverageData >= 5X There is a 6.57% of reference with a coverageData >= 6X There is a 5.74% of reference with a coverageData >= 7X There is a 5.07% of reference with a coverageData >= 8X There is a 4.52% of reference with a coverageData >= 9X There is a 4.07% of reference with a coverageData >= 10X There is a 3.68% of reference with a coverageData >= 11X There is a 3.35% of reference with a coverageData >= 12X There is a 3.06% of reference with a coverageData >= 13X There is a 2.82% of reference with a coverageData >= 14X There is a 2.6% of reference with a coverageData >= 15X There is a 2.4% of reference with a coverageData >= 16X There is a 2.23% of reference with a coverageData >= 17X There is a 2.08% of reference with a coverageData >= 18X There is a 1.94% of reference with a coverageData >= 19X There is a 1.82% of reference with a coverageData >= 20X There is a 1.71% of reference with a coverageData >= 21X There is a 1.6% of reference with a coverageData >= 22X There is a 1.51% of reference with a coverageData >= 23X There is a 1.43% of reference with a coverageData >= 24X There is a 1.35% of reference with a coverageData >= 25X There is a 1.28% of reference with a coverageData >= 26X There is a 1.21% of reference with a coverageData >= 27X There is a 1.15% of reference with a coverageData >= 28X There is a 1.09% of reference with a coverageData >= 29X There is a 1.04% of reference with a coverageData >= 30X There is a 0.99% of reference with a coverageData >= 31X There is a 0.94% of reference with a coverageData >= 32X There is a 0.9% of reference with a coverageData >= 33X There is a 0.86% of reference with a coverageData >= 34X There is a 0.82% of reference with a coverageData >= 35X There is a 0.79% of reference with a coverageData >= 36X There is a 0.75% of reference with a coverageData >= 37X There is a 0.72% of reference with a coverageData >= 38X There is a 0.69% of reference with a coverageData >= 39X There is a 0.66% of reference with a coverageData >= 40X There is a 0.64% of reference with a coverageData >= 41X There is a 0.61% of reference with a coverageData >= 42X There is a 0.59% of reference with a coverageData >= 43X There is a 0.57% of reference with a coverageData >= 44X There is a 0.55% of reference with a coverageData >= 45X There is a 0.53% of reference with a coverageData >= 46X There is a 0.51% of reference with a coverageData >= 47X There is a 0.49% of reference with a coverageData >= 48X There is a 0.47% of reference with a coverageData >= 49X There is a 0.46% of reference with a coverageData >= 50X There is a 0.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 506092625 2.0304568268257195 20.929424982618496 chr2 243199373 455714998 1.8738329477518842 106.34405432679789 chr3 198022430 311300910 1.5720487320552525 14.803605076631992 chr4 191154276 227080309 1.1879426071536061 15.04038597235901 chr5 180915260 272866407 1.5082553400967944 12.876335566591763 chr6 171115067 264707099 1.5469537758472198 14.669713870715736 chr7 159138663 252885603 1.5890896544732187 19.744611212386005 chr8 146364022 243945613 1.6667047657381266 16.850093331458247 chr9 141213431 246664464 1.746749315934403 23.33741693093775 chr10 135534747 279153558 2.0596456936611243 22.608679023710117 chr11 135006516 290451766 2.15139072250409 26.169555307815884 chr12 133851895 246411084 1.840923387748825 21.47791060014926 chr13 115169878 127503552 1.1070911440923814 13.993378032721056 chr14 107349540 169512806 1.5790734268633102 17.77324040625993 chr15 102531392 190537365 1.8583319828526272 20.044643133326822 chr16 90354753 211115648 2.3365195630605067 31.481788837434948 chr17 81195210 216358718 2.664673421005993 22.75870903333668 chr18 78077248 122006655 1.5626403097609178 14.980307144273574 chr19 59128983 148543258 2.512190307754828 17.142015151798148 chr20 63025520 179324359 2.845265838346118 20.98059159654119 chr21 48129895 68227619 1.4175725710600449 14.69784365525734 chr22 51304566 129669938 2.527454145114491 15.510423274180624 chrMT 16571 35489 2.14163297326655 7.994053620262637 chrX 155270560 8512728 0.05482512589637083 1.8492388939811706 chrY 59373566 39282350 0.6616134526937459 8.990849176245124