BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960910.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 = 137,022,420 number of mapped reads = 130,410,427 (95.17%) number of supplementary alignments = 2,063,357 (1.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 65,468,754 number of mapped paired reads (second in pair) = 64,941,673 number of mapped paired reads (both in pair) = 127,584,026 number of mapped paired reads (singletons) = 2,826,401 number of mapped bases = 11,341,198,079 bp number of sequenced bases = 11,338,100,436 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,584,655 duplication rate = 5.78% >>>>>>> Insert size mean insert size = 151,836.1588 std insert size = 4,006,502.0825 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.3722 >>>>>>> ACTG content number of A's = 3,291,210,377 bp (29.03%) number of C's = 2,333,064,817 bp (20.58%) number of T's = 3,359,340,165 bp (29.63%) number of G's = 2,352,872,661 bp (20.75%) number of N's = 1,612,416 bp (0.01%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 181,572,538 number of insertions = 1,743,608 mapped reads with insertion percentage = 1.31% number of deletions = 1,461,875 mapped reads with deletion percentage = 1.09% homopolymer indels = 36.84% >>>>>>> Coverage mean coverageData = 3.6635X std coverageData = 49.4861X There is a 83.96% of reference with a coverageData >= 1X There is a 71.76% of reference with a coverageData >= 2X There is a 56.98% of reference with a coverageData >= 3X There is a 42.83% of reference with a coverageData >= 4X There is a 30.65% of reference with a coverageData >= 5X There is a 21.13% of reference with a coverageData >= 6X There is a 14.13% of reference with a coverageData >= 7X There is a 9.23% of reference with a coverageData >= 8X There is a 5.93% of reference with a coverageData >= 9X There is a 3.77% of reference with a coverageData >= 10X There is a 2.4% of reference with a coverageData >= 11X There is a 1.53% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.67% of reference with a coverageData >= 14X There is a 0.46% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1047985785 4.204546334911639 126.96512265099473 chr2 243199373 981758587 4.0368467027256685 66.59044461902725 chr3 198022430 783761267 3.9579418705244653 8.17970134887553 chr4 191154276 687194196 3.594971613399849 22.297104696145986 chr5 180915260 553997492 3.062193272142991 4.9285937121858 chr6 171115067 566513243 3.31071514000576 15.468477194462864 chr7 159138663 642419475 4.036853539482106 32.6936551058572 chr8 146364022 589827845 4.029869068506467 40.61772620911641 chr9 141213431 541603208 3.8353519503396245 38.33927707166286 chr10 135534747 549065827 4.051107477258212 83.60576115163907 chr11 135006516 513510399 3.8035971463777347 23.7000949452241 chr12 133851895 424310980 3.1700035326358287 4.637337756351529 chr13 115169878 354445250 3.0775863980684255 3.0559358818111257 chr14 107349540 249690203 2.325955034367171 18.714086635218766 chr15 102531392 295375361 2.880828546636722 3.5875113905655334 chr16 90354753 398793433 4.413640896124192 42.217662839822076 chr17 81195210 225189049 2.7734277551594486 12.330494123734342 chr18 78077248 439274562 5.626153242491334 46.923671052801765 chr19 59128983 226753797 3.8349010163087027 57.433112995342505 chr20 63025520 212332219 3.3689879750297975 10.152080283080345 chr21 48129895 160180393 3.3280852368366896 15.024353144917734 chr22 51304566 119073513 2.3209145361447945 3.5591583649480385 chrMT 16571 2395379 144.5524711845996 30.002898110420194 chrX 155270560 740168525 4.766959847378666 16.493319642793416 chrY 59373566 35578091 0.5992244259002398 26.897185911604513