BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504629.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 = 570,873,916 number of mapped reads = 467,572,140 (81.9%) number of supplementary alignments = 4,090,396 (0.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 238,883,408 number of mapped paired reads (second in pair) = 228,688,732 number of mapped paired reads (both in pair) = 442,366,498 number of mapped paired reads (singletons) = 25,205,642 number of mapped bases = 43,752,778,467 bp number of sequenced bases = 43,717,173,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,566,329 duplication rate = 22.22% >>>>>>> Insert size mean insert size = 105,858.3658 std insert size = 3,037,604.493 median insert size = 353 >>>>>>> Mapping quality mean mapping quality = 51.2733 >>>>>>> ACTG content number of A's = 11,896,554,533 bp (27.21%) number of C's = 9,912,479,769 bp (22.67%) number of T's = 12,065,438,836 bp (27.6%) number of G's = 9,782,485,515 bp (22.38%) number of N's = 60,214,541 bp (0.14%) GC percentage = 45.05% >>>>>>> Mismatches and indels general error rate = 0.0275 number of mismatches = 1,154,931,727 number of insertions = 12,024,457 mapped reads with insertion percentage = 2.4% number of deletions = 11,055,191 mapped reads with deletion percentage = 2.21% homopolymer indels = 33.11% >>>>>>> Coverage mean coverageData = 14.1334X std coverageData = 295.4324X There is a 86.93% of reference with a coverageData >= 1X There is a 81.53% of reference with a coverageData >= 2X There is a 75.77% of reference with a coverageData >= 3X There is a 70.23% of reference with a coverageData >= 4X There is a 64.96% of reference with a coverageData >= 5X There is a 60.06% of reference with a coverageData >= 6X There is a 55.52% of reference with a coverageData >= 7X There is a 51.35% of reference with a coverageData >= 8X There is a 47.51% of reference with a coverageData >= 9X There is a 43.97% of reference with a coverageData >= 10X There is a 40.72% of reference with a coverageData >= 11X There is a 37.73% of reference with a coverageData >= 12X There is a 34.97% of reference with a coverageData >= 13X There is a 32.42% of reference with a coverageData >= 14X There is a 30.06% of reference with a coverageData >= 15X There is a 27.88% of reference with a coverageData >= 16X There is a 25.87% of reference with a coverageData >= 17X There is a 24% of reference with a coverageData >= 18X There is a 22.27% of reference with a coverageData >= 19X There is a 20.67% of reference with a coverageData >= 20X There is a 19.19% of reference with a coverageData >= 21X There is a 17.82% of reference with a coverageData >= 22X There is a 16.55% of reference with a coverageData >= 23X There is a 15.37% of reference with a coverageData >= 24X There is a 14.28% of reference with a coverageData >= 25X There is a 13.27% of reference with a coverageData >= 26X There is a 12.33% of reference with a coverageData >= 27X There is a 11.47% of reference with a coverageData >= 28X There is a 10.67% of reference with a coverageData >= 29X There is a 9.92% of reference with a coverageData >= 30X There is a 9.24% of reference with a coverageData >= 31X There is a 8.6% of reference with a coverageData >= 32X There is a 8.01% of reference with a coverageData >= 33X There is a 7.47% of reference with a coverageData >= 34X There is a 6.96% of reference with a coverageData >= 35X There is a 6.49% of reference with a coverageData >= 36X There is a 6.06% of reference with a coverageData >= 37X There is a 5.66% of reference with a coverageData >= 38X There is a 5.29% of reference with a coverageData >= 39X There is a 4.94% of reference with a coverageData >= 40X There is a 4.62% of reference with a coverageData >= 41X There is a 4.33% of reference with a coverageData >= 42X There is a 4.05% of reference with a coverageData >= 43X There is a 3.8% of reference with a coverageData >= 44X There is a 3.56% of reference with a coverageData >= 45X There is a 3.34% of reference with a coverageData >= 46X There is a 3.14% of reference with a coverageData >= 47X There is a 2.95% of reference with a coverageData >= 48X There is a 2.78% of reference with a coverageData >= 49X There is a 2.62% of reference with a coverageData >= 50X There is a 2.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3091924158 12.404880459655907 100.12134500803914 chr2 243199373 3313290842 13.623763914884764 305.43086716201503 chr3 198022430 2269919673 11.462942218212351 34.94823332889423 chr4 191154276 3167217646 16.568908173416954 746.3399163361966 chr5 180915260 2725340462 15.064182324918306 42.79978696103737 chr6 171115067 1317076275 7.697021063609787 31.109071219315926 chr7 159138663 2062596781 12.961003580883421 48.11021194584203 chr8 146364022 2444413688 16.700919082423137 226.66614622844943 chr9 141213431 1149158910 8.137745127090637 140.97548623243406 chr10 135534747 3259026462 24.045689641490974 726.2591609900712 chr11 135006516 1780278371 13.186610718848563 34.93634698587987 chr12 133851895 1661627970 12.41392936573666 30.94617652839982 chr13 115169878 687668497 5.970905838764542 14.878135875754758 chr14 107349540 1129038475 10.517403940436074 36.731692595760556 chr15 102531392 1490421871 14.536249259153724 24.29962819539145 chr16 90354753 2300659050 25.462512746839117 300.9958549116436 chr17 81195210 1383535665 17.03962173384366 95.4610487611603 chr18 78077248 728367929 9.328811499606134 375.3386983080632 chr19 59128983 1649440905 27.895641381148057 60.899428072936196 chr20 63025520 1273553510 20.2069496610262 201.64476922523423 chr21 48129895 828878946 17.221706924563204 268.8932347978549 chr22 51304566 751825477 14.654163081703098 39.468262562440096 chrMT 16571 14343796 865.5962826624826 400.12454658256314 chrX 155270560 2560325376 16.48944510794577 33.50206148362245 chrY 59373566 712847732 12.00614650634257 693.5471110789103