BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695958.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 344,045,402 number of mapped reads = 339,094,426 (98.56%) number of supplementary alignments = 5,264,680 (1.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 170,636,026 number of mapped paired reads (second in pair) = 168,458,400 number of mapped paired reads (both in pair) = 335,739,968 number of mapped paired reads (singletons) = 3,354,458 number of mapped bases = 33,516,302,256 bp number of sequenced bases = 33,504,931,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,246,738 duplication rate = 13.5% >>>>>>> Insert size mean insert size = 80,496.2551 std insert size = 2,712,912.1101 median insert size = 323 >>>>>>> Mapping quality mean mapping quality = 53.8989 >>>>>>> ACTG content number of A's = 9,360,253,074 bp (27.94%) number of C's = 7,298,957,995 bp (21.78%) number of T's = 9,310,709,377 bp (27.79%) number of G's = 7,524,953,735 bp (22.46%) number of N's = 10,056,843 bp (0.03%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 167,609,457 number of insertions = 5,514,138 mapped reads with insertion percentage = 1.57% number of deletions = 4,335,798 mapped reads with deletion percentage = 1.23% homopolymer indels = 40.39% >>>>>>> Coverage mean coverageData = 10.8267X std coverageData = 40.8611X There is a 87.39% of reference with a coverageData >= 1X There is a 80.94% of reference with a coverageData >= 2X There is a 73.97% of reference with a coverageData >= 3X There is a 67.07% of reference with a coverageData >= 4X There is a 60.57% of reference with a coverageData >= 5X There is a 54.58% of reference with a coverageData >= 6X There is a 49.17% of reference with a coverageData >= 7X There is a 44.32% of reference with a coverageData >= 8X There is a 39.98% of reference with a coverageData >= 9X There is a 36.13% of reference with a coverageData >= 10X There is a 32.71% of reference with a coverageData >= 11X There is a 29.67% of reference with a coverageData >= 12X There is a 26.97% of reference with a coverageData >= 13X There is a 24.56% of reference with a coverageData >= 14X There is a 22.42% of reference with a coverageData >= 15X There is a 20.5% of reference with a coverageData >= 16X There is a 18.79% of reference with a coverageData >= 17X There is a 17.26% of reference with a coverageData >= 18X There is a 15.88% of reference with a coverageData >= 19X There is a 14.64% of reference with a coverageData >= 20X There is a 13.52% of reference with a coverageData >= 21X There is a 12.5% of reference with a coverageData >= 22X There is a 11.59% of reference with a coverageData >= 23X There is a 10.75% of reference with a coverageData >= 24X There is a 10% of reference with a coverageData >= 25X There is a 9.31% of reference with a coverageData >= 26X There is a 8.67% of reference with a coverageData >= 27X There is a 8.1% of reference with a coverageData >= 28X There is a 7.57% of reference with a coverageData >= 29X There is a 7.08% of reference with a coverageData >= 30X There is a 6.64% of reference with a coverageData >= 31X There is a 6.23% of reference with a coverageData >= 32X There is a 5.85% of reference with a coverageData >= 33X There is a 5.5% of reference with a coverageData >= 34X There is a 5.18% of reference with a coverageData >= 35X There is a 4.88% of reference with a coverageData >= 36X There is a 4.6% of reference with a coverageData >= 37X There is a 4.35% of reference with a coverageData >= 38X There is a 4.11% of reference with a coverageData >= 39X There is a 3.88% of reference with a coverageData >= 40X There is a 3.68% of reference with a coverageData >= 41X There is a 3.49% of reference with a coverageData >= 42X There is a 3.31% of reference with a coverageData >= 43X There is a 3.14% of reference with a coverageData >= 44X There is a 2.98% of reference with a coverageData >= 45X There is a 2.83% of reference with a coverageData >= 46X There is a 2.69% of reference with a coverageData >= 47X There is a 2.56% of reference with a coverageData >= 48X There is a 2.44% of reference with a coverageData >= 49X There is a 2.33% of reference with a coverageData >= 50X There is a 2.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2955287385 11.856690158457017 33.70757545435051 chr2 243199373 2651344773 10.901939179752738 83.53325464251755 chr3 198022430 1951895960 9.856943781570603 18.160306542196402 chr4 191154276 1890366173 9.889217299015586 23.87533143151413 chr5 180915260 1700064767 9.397022489976798 19.14316650749071 chr6 171115067 2132763267 12.463912759944161 30.727124611679155 chr7 159138663 1666640421 10.472881885403298 23.21400207886106 chr8 146364022 1467229710 10.024524401222044 29.2057469088213 chr9 141213431 1261871313 8.93591568496059 61.59413450112793 chr10 135534747 1523001597 11.236982624094175 59.568421371367734 chr11 135006516 1783133578 13.207759379554687 27.31942023534004 chr12 133851895 1820056836 13.59754253759351 20.05136174344843 chr13 115169878 917369641 7.965360881948664 18.831310077381143 chr14 107349540 1113327861 10.371053858265253 42.856503682061124 chr15 102531392 996194045 9.715990640212901 22.214517127037116 chr16 90354753 1213013356 13.425008820509973 60.139567170753 chr17 81195210 1419720821 17.485278023174025 34.460831625405184 chr18 78077248 883044017 11.30987630352955 42.33352203317387 chr19 59128983 1197080928 20.245248053733647 36.88242574871136 chr20 63025520 931393003 14.778029645768889 22.552421837578194 chr21 48129895 425712005 8.845064070885673 25.209827262307652 chr22 51304566 592670786 11.552008567814413 24.163606906797945 chrMT 16571 22352843 1348.913342586446 470.33703344311147 chrX 155270560 757496903 4.878561029212492 12.451114859248761 chrY 59373566 243270267 4.097282400049881 70.90237563317513