BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124901.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,221,068 number of mapped reads = 5,160,244 (98.84%) number of supplementary alignments = 21,549 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,581,223 number of mapped paired reads (second in pair) = 2,579,021 number of mapped paired reads (both in pair) = 5,144,548 number of mapped paired reads (singletons) = 15,696 number of mapped bases = 467,234,222 bp number of sequenced bases = 466,988,351 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 301,694 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 50,322.7782 std insert size = 2,153,178.4943 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 53.5836 >>>>>>> ACTG content number of A's = 131,358,799 bp (28.13%) number of C's = 92,216,927 bp (19.75%) number of T's = 136,093,801 bp (29.14%) number of G's = 107,312,058 bp (22.98%) number of N's = 6,766 bp (0%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 3,244,270 number of insertions = 60,135 mapped reads with insertion percentage = 1.13% number of deletions = 146,233 mapped reads with deletion percentage = 2.78% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.1509X std coverageData = 1.2342X There is a 9.6% of reference with a coverageData >= 1X There is a 2.86% of reference with a coverageData >= 2X There is a 0.92% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 35253644 0.1414385402875285 1.31334198141906 chr2 243199373 44194913 0.18172297261638087 1.6322574114345252 chr3 198022430 28754650 0.1452090553580218 0.5748184811435774 chr4 191154276 24638923 0.12889548439920853 0.8386071246345751 chr5 180915260 30563643 0.16893899939673415 0.6350147344880762 chr6 171115067 24509410 0.14323350029720058 0.8738797486917284 chr7 159138663 27419636 0.17230027878266138 1.5381163382284462 chr8 146364022 27103588 0.18517930588160525 0.7198714382401665 chr9 141213431 14687647 0.10401026939144337 1.3296763075234888 chr10 135534747 26630387 0.1964838359863541 3.0467376309769216 chr11 135006516 24057864 0.1781977989862356 0.9204168075713772 chr12 133851895 20354241 0.15206539287322007 0.6415687066775015 chr13 115169878 14493663 0.12584595253283154 0.5066460999646055 chr14 107349540 11818990 0.11009818952181817 0.5706228268248164 chr15 102531392 14652118 0.14290372649968508 0.5707240381072683 chr16 90354753 15266836 0.1689654998005473 1.8198038687534934 chr17 81195210 17795013 0.2191633348814542 1.4466370846575805 chr18 78077248 8654724 0.11084822047006575 1.6171806757806064 chr19 59128983 9763473 0.16512161218805335 0.9514216257081809 chr20 63025520 11313836 0.17951198181308142 0.8008087973953395 chr21 48129895 4137837 0.08597228396197415 0.5345771135919107 chr22 51304566 6659207 0.12979755057278916 0.5833156984771863 chrMT 16571 300890 18.157624766157745 10.407178963083208 chrX 155270560 23096816 0.14875206220676992 0.8333678297885273 chrY 59373566 1112273 0.018733471390281663 1.2273642909405722