BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617419.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 = 30,305,443 (94.7%) number of supplementary alignments = 501,291 (1.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,331,113 number of mapped paired reads (second in pair) = 14,974,330 number of mapped paired reads (both in pair) = 29,705,800 number of mapped paired reads (singletons) = 599,643 number of mapped bases = 2,987,256,683 bp number of sequenced bases = 2,986,583,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,447,853 duplication rate = 4.26% >>>>>>> Insert size mean insert size = 60,414.3678 std insert size = 2,358,857.457 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 53.8987 >>>>>>> ACTG content number of A's = 888,941,986 bp (29.76%) number of C's = 601,886,046 bp (20.15%) number of T's = 882,525,043 bp (29.55%) number of G's = 613,012,882 bp (20.53%) number of N's = 218,031 bp (0.01%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 24,160,433 number of insertions = 248,202 mapped reads with insertion percentage = 0.81% number of deletions = 295,912 mapped reads with deletion percentage = 0.96% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 0.965X std coverageData = 2.9746X There is a 29.77% of reference with a coverageData >= 1X There is a 17.1% of reference with a coverageData >= 2X There is a 10.97% of reference with a coverageData >= 3X There is a 7.6% of reference with a coverageData >= 4X There is a 5.53% of reference with a coverageData >= 5X There is a 4.17% of reference with a coverageData >= 6X There is a 3.23% of reference with a coverageData >= 7X There is a 2.56% of reference with a coverageData >= 8X There is a 2.06% of reference with a coverageData >= 9X There is a 1.69% of reference with a coverageData >= 10X There is a 1.4% of reference with a coverageData >= 11X There is a 1.17% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.85% of reference with a coverageData >= 14X There is a 0.73% of reference with a coverageData >= 15X There is a 0.64% of reference with a coverageData >= 16X There is a 0.56% of reference with a coverageData >= 17X There is a 0.49% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192625108 0.7728169632123003 2.7974389365085472 chr2 243199373 297827691 1.2246235971998167 3.165179911761854 chr3 198022430 251597313 1.270549568551401 3.469477674900849 chr4 191154276 142583988 0.7459105335420276 2.291636423242282 chr5 180915260 190685946 1.0540069754204262 2.895749495119075 chr6 171115067 136508706 0.7977597086760337 2.624728220619406 chr7 159138663 223099158 1.4019167548240619 3.2777462926665026 chr8 146364022 131804151 0.9005228825974733 3.2968397073752347 chr9 141213431 119286601 0.8447256054560419 2.6356379942529196 chr10 135534747 95801073 0.7068377306964686 2.4619863683850025 chr11 135006516 221905609 1.6436659175768968 3.8848347147330022 chr12 133851895 142411150 1.0639457140296744 2.8454347119929393 chr13 115169878 128909674 1.1193002566174464 2.7975477369142427 chr14 107349540 86915571 0.8096501484775808 2.9509562671596106 chr15 102531392 68795574 0.6709708378873858 2.4156946532942736 chr16 90354753 75870012 0.8396903259754359 3.3908212368616018 chr17 81195210 93023850 1.1456815001771656 3.7952576910414484 chr18 78077248 42643820 0.5461747319782583 2.0233551150339206 chr19 59128983 43506471 0.7357892659848386 2.399951443871339 chr20 63025520 102970696 1.633793675958564 4.850130100938061 chr21 48129895 40668168 0.8449668963541267 2.528453578444371 chr22 51304566 24517038 0.4778724373187369 2.1343867152512375 chrMT 16571 188210 11.357793736044897 6.261138495815415 chrX 155270560 130689503 0.8416888752124034 2.5974783392027336 chrY 59373566 2421602 0.040785860832411515 0.6541057191933612