BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006229.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 2,492,084 number of mapped reads = 2,187,945 (87.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,103,475 number of mapped paired reads (second in pair) = 1,084,470 number of mapped paired reads (both in pair) = 2,025,428 number of mapped paired reads (singletons) = 162,517 number of mapped bases = 84,533,387 bp number of sequenced bases = 84,523,380 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,591 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 82,617.1364 std insert size = 2,811,437.7632 median insert size = 132 >>>>>>> Mapping quality mean mapping quality = 47.4351 >>>>>>> ACTG content number of A's = 22,961,787 bp (27.17%) number of C's = 18,818,067 bp (22.26%) number of T's = 23,447,361 bp (27.74%) number of G's = 19,292,712 bp (22.83%) number of N's = 3,453 bp (0%) GC percentage = 45.09% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 341,150 number of insertions = 2,534 mapped reads with insertion percentage = 0.12% number of deletions = 7,518 mapped reads with deletion percentage = 0.34% homopolymer indels = 40.97% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.2118X There is a 2.38% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% 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 6957348 0.027913061849502874 0.23038276204893 chr2 243199373 7059480 0.029027541941894726 0.2078312681842473 chr3 198022430 5660725 0.0285862818671602 0.18839264015655316 chr4 191154276 5291777 0.0276832781914855 0.20133606079506522 chr5 180915260 4876382 0.02695395623343216 0.18366790718004689 chr6 171115067 4729068 0.02763677145975696 0.1906296670990585 chr7 159138663 4770118 0.029974601458100724 0.22663162105842016 chr8 146364022 4169035 0.02848401501292442 0.3733471788799888 chr9 141213431 3418459 0.024207746924582548 0.18504091431737463 chr10 135534747 3943511 0.02909594098404891 0.22521035725990812 chr11 135006516 3891190 0.02882223847625251 0.1990999750238743 chr12 133851895 3708815 0.027708348843324182 0.18746445271696874 chr13 115169878 2417410 0.020989950167351917 0.16218404290879768 chr14 107349540 2643194 0.024622313239535076 0.20416356899297014 chr15 102531392 2476399 0.02415259318824034 0.17336801958400355 chr16 90354753 2737684 0.03029928043741097 0.20931705300032186 chr17 81195210 2573997 0.03170134051011137 0.20599866066971864 chr18 78077248 2189358 0.02804092172920849 0.22440516815240155 chr19 59128983 1995163 0.03374255566005591 0.2274260592052681 chr20 63025520 1957654 0.031061290727946392 0.20635383255444048 chr21 48129895 1061779 0.022060696371766445 0.1801808835380292 chr22 51304566 1245774 0.024281932333274196 0.18290314279784498 chrMT 16571 858 0.0517772011345121 0.2521496693665635 chrX 155270560 4499030 0.028975421998864433 0.19297218908454356 chrY 59373566 259179 0.004365225427086525 0.12486209224983988