BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163019.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 = 93,316,692 number of mapped reads = 91,393,240 (97.94%) number of supplementary alignments = 547,071 (0.59%) number of secondary alignments = 0 number of mapped bases = 8,911,589,622 bp number of sequenced bases = 8,910,453,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,444,545 duplication rate = 45.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0398 >>>>>>> ACTG content number of A's = 2,136,456,633 bp (23.98%) number of C's = 2,320,052,552 bp (26.04%) number of T's = 2,129,833,645 bp (23.9%) number of G's = 2,322,079,583 bp (26.06%) number of N's = 2,031,205 bp (0.02%) GC percentage = 52.1% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 38,943,193 number of insertions = 623,666 mapped reads with insertion percentage = 0.67% number of deletions = 512,002 mapped reads with deletion percentage = 0.55% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 2.8787X std coverageData = 34.933X There is a 12.39% of reference with a coverageData >= 1X There is a 7.81% of reference with a coverageData >= 2X There is a 5.36% of reference with a coverageData >= 3X There is a 4.67% of reference with a coverageData >= 4X There is a 4.15% of reference with a coverageData >= 5X There is a 3.86% of reference with a coverageData >= 6X There is a 3.63% of reference with a coverageData >= 7X There is a 3.45% of reference with a coverageData >= 8X There is a 3.29% of reference with a coverageData >= 9X There is a 3.16% of reference with a coverageData >= 10X There is a 3.04% of reference with a coverageData >= 11X There is a 2.94% of reference with a coverageData >= 12X There is a 2.84% of reference with a coverageData >= 13X There is a 2.75% of reference with a coverageData >= 14X There is a 2.67% of reference with a coverageData >= 15X There is a 2.59% of reference with a coverageData >= 16X There is a 2.52% of reference with a coverageData >= 17X There is a 2.45% of reference with a coverageData >= 18X There is a 2.39% of reference with a coverageData >= 19X There is a 2.33% of reference with a coverageData >= 20X There is a 2.27% of reference with a coverageData >= 21X There is a 2.21% of reference with a coverageData >= 22X There is a 2.16% of reference with a coverageData >= 23X There is a 2.11% of reference with a coverageData >= 24X There is a 2.06% of reference with a coverageData >= 25X There is a 2.02% of reference with a coverageData >= 26X There is a 1.98% of reference with a coverageData >= 27X There is a 1.93% of reference with a coverageData >= 28X There is a 1.89% of reference with a coverageData >= 29X There is a 1.85% of reference with a coverageData >= 30X There is a 1.82% of reference with a coverageData >= 31X There is a 1.78% of reference with a coverageData >= 32X There is a 1.75% of reference with a coverageData >= 33X There is a 1.71% of reference with a coverageData >= 34X There is a 1.68% of reference with a coverageData >= 35X There is a 1.65% of reference with a coverageData >= 36X There is a 1.62% of reference with a coverageData >= 37X There is a 1.59% of reference with a coverageData >= 38X There is a 1.56% of reference with a coverageData >= 39X There is a 1.53% of reference with a coverageData >= 40X There is a 1.51% of reference with a coverageData >= 41X There is a 1.48% of reference with a coverageData >= 42X There is a 1.45% of reference with a coverageData >= 43X There is a 1.43% of reference with a coverageData >= 44X There is a 1.41% of reference with a coverageData >= 45X There is a 1.38% of reference with a coverageData >= 46X There is a 1.36% of reference with a coverageData >= 47X There is a 1.34% of reference with a coverageData >= 48X There is a 1.32% of reference with a coverageData >= 49X There is a 1.3% of reference with a coverageData >= 50X There is a 1.28% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1312060877 5.264022499667112 47.9895284870082 chr2 243199373 368111686 1.5136210322384342 16.40877401116478 chr3 198022430 363458813 1.8354426465729161 18.854222776545317 chr4 191154276 192610842 1.0076198452395593 17.07743979564791 chr5 180915260 506899829 2.8018633088220417 49.75137155587366 chr6 171115067 508854353 2.973755391160265 30.256652623384426 chr7 159138663 555089745 3.48808852943549 36.446427331941166 chr8 146364022 421686722 2.8810818139446863 45.22277785748265 chr9 141213431 233993749 1.657021908914599 18.20335085492557 chr10 135534747 195786890 1.4445512633007682 14.44729001522046 chr11 135006516 513093640 3.800510191671045 32.42104204566917 chr12 133851895 242066197 1.8084629806697918 17.74522365456356 chr13 115169878 123661645 1.073732534473988 13.988951093682106 chr14 107349540 262393868 2.444294293203306 23.623446389167473 chr15 102531392 398414874 3.8857843069174365 31.932438921287254 chr16 90354753 419595838 4.643871230548325 35.95495945200677 chr17 81195210 292580754 3.60342382266146 30.1680003611759 chr18 78077248 157020981 2.011097791254118 23.03333804412884 chr19 59128983 865898026 14.644223222983557 108.81779189088756 chr20 63025520 236007468 3.744633411989302 31.85124894556073 chr21 48129895 134205553 2.788403195145138 67.2785012990585 chr22 51304566 111801480 2.1791721228087186 19.910004412176864 chrMT 16571 7590 0.4580290869591455 0.9127489095980129 chrX 155270560 487217883 3.137863887397585 35.7036163631528 chrY 59373566 9070319 0.15276695693164194 9.398631986424023