BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617421.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 27,423,783 (85.7%) number of supplementary alignments = 394,403 (1.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,392,501 number of mapped paired reads (second in pair) = 13,031,282 number of mapped paired reads (both in pair) = 25,785,654 number of mapped paired reads (singletons) = 1,638,129 number of mapped bases = 2,664,330,959 bp number of sequenced bases = 2,663,748,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,163,531 duplication rate = 3.84% >>>>>>> Insert size mean insert size = 56,923.1569 std insert size = 2,274,432.0949 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 53.486 >>>>>>> ACTG content number of A's = 796,160,389 bp (29.89%) number of C's = 533,830,283 bp (20.04%) number of T's = 788,320,250 bp (29.59%) number of G's = 545,182,291 bp (20.47%) number of N's = 255,712 bp (0.01%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 43,089,407 number of insertions = 224,828 mapped reads with insertion percentage = 0.81% number of deletions = 260,660 mapped reads with deletion percentage = 0.93% homopolymer indels = 43.71% >>>>>>> Coverage mean coverageData = 0.8607X std coverageData = 2.6448X There is a 28.27% of reference with a coverageData >= 1X There is a 15.79% of reference with a coverageData >= 2X There is a 9.89% of reference with a coverageData >= 3X There is a 6.72% of reference with a coverageData >= 4X There is a 4.81% of reference with a coverageData >= 5X There is a 3.57% of reference with a coverageData >= 6X There is a 2.73% of reference with a coverageData >= 7X There is a 2.14% of reference with a coverageData >= 8X There is a 1.71% of reference with a coverageData >= 9X There is a 1.39% of reference with a coverageData >= 10X There is a 1.14% of reference with a coverageData >= 11X There is a 0.95% of reference with a coverageData >= 12X There is a 0.8% of reference with a coverageData >= 13X There is a 0.68% of reference with a coverageData >= 14X There is a 0.58% of reference with a coverageData >= 15X There is a 0.5% of reference with a coverageData >= 16X There is a 0.43% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171010467 0.6860984591087539 2.4786381482263673 chr2 243199373 266186121 1.094518121969007 2.8249199226426684 chr3 198022430 225379216 1.1381499358431264 3.08540135793234 chr4 191154276 128946026 0.6745652187241681 2.088564948114958 chr5 180915260 171356635 0.9471651810908599 2.6129675970266355 chr6 171115067 122612512 0.7165500627715033 2.360176665840201 chr7 159138663 199762554 1.255273547195756 2.9481437870147458 chr8 146364022 118092192 0.8068389375088367 2.913320647876742 chr9 141213431 106382041 0.7533422298902999 2.343696431632013 chr10 135534747 85403923 0.6301256680694582 2.1768825518514334 chr11 135006516 197274699 1.4612235382772192 3.4580157872065453 chr12 133851895 126662084 0.9462853252843376 2.5277141533875733 chr13 115169878 116254615 1.0094185825220723 2.534854362539405 chr14 107349540 77118223 0.7183842893038945 2.602244564693412 chr15 102531392 60883649 0.5938049587778931 2.16328887332198 chr16 90354753 66482084 0.7357895605115539 2.9667067066482162 chr17 81195210 81281610 1.0010641021804119 3.2569136861410444 chr18 78077248 38429020 0.492192296531763 1.8170197539337447 chr19 59128983 37390965 0.6323627281057751 2.0674723886299713 chr20 63025520 89868645 1.4259088223310177 4.222110023292365 chr21 48129895 36564009 0.7596943438168731 2.295627917841462 chr22 51304566 21146025 0.4121665311426667 1.8607238084519668 chrMT 16571 158239 9.549152133244826 4.836758284252359 chrX 155270560 117531115 0.7569439757285605 2.3267196347551278 chrY 59373566 2154290 0.03628365525493281 0.5586210125561886