BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504671.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 214,985,014 number of mapped reads = 213,906,381 (99.5%) number of supplementary alignments = 2,754,440 (1.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 107,090,062 number of mapped paired reads (second in pair) = 106,816,319 number of mapped paired reads (both in pair) = 213,526,252 number of mapped paired reads (singletons) = 380,129 number of mapped bases = 19,879,346,603 bp number of sequenced bases = 19,874,315,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,172,268 duplication rate = 33.57% >>>>>>> Insert size mean insert size = 28,346.612 std insert size = 1,573,557.6859 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 53.1525 >>>>>>> ACTG content number of A's = 5,973,042,410 bp (30.05%) number of C's = 3,936,035,827 bp (19.8%) number of T's = 6,054,330,518 bp (30.46%) number of G's = 3,894,489,676 bp (19.6%) number of N's = 16,416,745 bp (0.08%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 102,712,131 number of insertions = 2,189,138 mapped reads with insertion percentage = 1.01% number of deletions = 2,680,827 mapped reads with deletion percentage = 1.23% homopolymer indels = 50.37% >>>>>>> Coverage mean coverageData = 6.4216X std coverageData = 806.64X There is a 43.52% of reference with a coverageData >= 1X There is a 34.71% of reference with a coverageData >= 2X There is a 27.07% of reference with a coverageData >= 3X There is a 22.88% of reference with a coverageData >= 4X There is a 19.62% of reference with a coverageData >= 5X There is a 17.24% of reference with a coverageData >= 6X There is a 15.32% of reference with a coverageData >= 7X There is a 13.77% of reference with a coverageData >= 8X There is a 12.48% of reference with a coverageData >= 9X There is a 11.4% of reference with a coverageData >= 10X There is a 10.46% of reference with a coverageData >= 11X There is a 9.66% of reference with a coverageData >= 12X There is a 8.95% of reference with a coverageData >= 13X There is a 8.33% of reference with a coverageData >= 14X There is a 7.78% of reference with a coverageData >= 15X There is a 7.29% of reference with a coverageData >= 16X There is a 6.85% of reference with a coverageData >= 17X There is a 6.45% of reference with a coverageData >= 18X There is a 6.09% of reference with a coverageData >= 19X There is a 5.76% of reference with a coverageData >= 20X There is a 5.46% of reference with a coverageData >= 21X There is a 5.19% of reference with a coverageData >= 22X There is a 4.93% of reference with a coverageData >= 23X There is a 4.7% of reference with a coverageData >= 24X There is a 4.48% of reference with a coverageData >= 25X There is a 4.28% of reference with a coverageData >= 26X There is a 4.1% of reference with a coverageData >= 27X There is a 3.93% of reference with a coverageData >= 28X There is a 3.77% of reference with a coverageData >= 29X There is a 3.62% of reference with a coverageData >= 30X There is a 3.47% of reference with a coverageData >= 31X There is a 3.34% of reference with a coverageData >= 32X There is a 3.22% of reference with a coverageData >= 33X There is a 3.1% of reference with a coverageData >= 34X There is a 2.99% of reference with a coverageData >= 35X There is a 2.89% of reference with a coverageData >= 36X There is a 2.79% of reference with a coverageData >= 37X There is a 2.69% of reference with a coverageData >= 38X There is a 2.61% of reference with a coverageData >= 39X There is a 2.52% of reference with a coverageData >= 40X There is a 2.44% of reference with a coverageData >= 41X There is a 2.37% of reference with a coverageData >= 42X There is a 2.29% of reference with a coverageData >= 43X There is a 2.22% of reference with a coverageData >= 44X There is a 2.16% of reference with a coverageData >= 45X There is a 2.1% of reference with a coverageData >= 46X There is a 2.04% of reference with a coverageData >= 47X There is a 1.98% of reference with a coverageData >= 48X There is a 1.93% of reference with a coverageData >= 49X There is a 1.87% of reference with a coverageData >= 50X There is a 1.82% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1369429340 5.494186271255067 79.50293389267478 chr2 243199373 1396755881 5.743254449097614 33.25052322714211 chr3 198022430 1187188309 5.995221394869258 58.23081529764425 chr4 191154276 1273623529 6.662804283802681 109.4120531654024 chr5 180915260 1159426138 6.408669661144118 38.481943974652374 chr6 171115067 1103417781 6.448396393989081 66.09178073585747 chr7 159138663 925885133 5.818103002411174 32.295009356689256 chr8 146364022 854048723 5.835100124537436 20.812648939744903 chr9 141213431 871908948 6.174405237700088 77.33252743497712 chr10 135534747 751676506 5.546005896185426 85.23524570038717 chr11 135006516 703373961 5.209926023126172 30.53012146624485 chr12 133851895 871944148 6.5142458237143375 71.74378321870796 chr13 115169878 645347154 5.603436985493724 100.80302743257089 chr14 107349540 525489580 4.895126518474136 33.18635678971805 chr15 102531392 515329430 5.026064895324936 36.95025386242762 chr16 90354753 393285123 4.352677750112382 21.53322921986453 chr17 81195210 573497187 7.0631898975321326 306.4330201056308 chr18 78077248 427548251 5.475964662586469 27.362607923430634 chr19 59128983 177944480 3.0094290645925703 15.033911964447173 chr20 63025520 251647149 3.992781796960977 15.57341585228503 chr21 48129895 207033890 4.301565378440988 25.827082053467148 chr22 51304566 101595839 1.9802494577188314 7.458982256698121 chrMT 16571 6185 0.3732424114416752 2.5928532260658823 chrX 155270560 3574176066 23.019019613248 3585.6623668747266 chrY 59373566 17767872 0.29925559802151686 4.055732785443048