BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927002.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 31,374,386 number of mapped reads = 29,794,167 (94.96%) number of supplementary alignments = 980,959 (3.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,918,705 number of mapped paired reads (second in pair) = 14,875,462 number of mapped paired reads (both in pair) = 29,297,108 number of mapped paired reads (singletons) = 497,059 number of mapped bases = 2,702,085,457 bp number of sequenced bases = 2,699,942,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,175,796 duplication rate = 8.3% >>>>>>> Insert size mean insert size = 337,567.7039 std insert size = 5,684,373.3362 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 52.7251 >>>>>>> ACTG content number of A's = 774,139,195 bp (28.67%) number of C's = 518,469,459 bp (19.2%) number of T's = 793,019,605 bp (29.37%) number of G's = 613,822,704 bp (22.73%) number of N's = 491,580 bp (0.02%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 26,158,772 number of insertions = 483,785 mapped reads with insertion percentage = 1.59% number of deletions = 1,468,720 mapped reads with deletion percentage = 4.8% homopolymer indels = 52.14% >>>>>>> Coverage mean coverageData = 0.8729X std coverageData = 3.2166X There is a 34.13% of reference with a coverageData >= 1X There is a 19.14% of reference with a coverageData >= 2X There is a 11.19% of reference with a coverageData >= 3X There is a 6.95% of reference with a coverageData >= 4X There is a 4.45% of reference with a coverageData >= 5X There is a 2.94% of reference with a coverageData >= 6X There is a 1.99% of reference with a coverageData >= 7X There is a 1.37% of reference with a coverageData >= 8X There is a 0.97% of reference with a coverageData >= 9X There is a 0.69% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 227989948 0.9147016247554304 4.062392434976375 chr2 243199373 228778829 0.940704847129684 5.150201874421199 chr3 198022430 179524797 0.9065881930647958 1.838488172509378 chr4 191154276 161666010 0.845735776269007 2.68059988726542 chr5 180915260 158301315 0.8750025564454872 1.775462672867964 chr6 171115067 153751112 0.8985246868997223 2.4513958544200403 chr7 159138663 136681322 0.8588819299053682 2.439759155212034 chr8 146364022 133079963 0.9092395875811612 2.1443074550229646 chr9 141213431 149692258 1.0600426385787625 4.425614297283048 chr10 135534747 127119322 0.9379094646482057 5.379362222822038 chr11 135006516 127693906 0.945835132876105 2.7974329809237113 chr12 133851895 119747291 0.8946252946213424 1.8827459357910508 chr13 115169878 80003101 0.6946529977221996 1.5732879770878185 chr14 107349540 81493443 0.7591410545401499 1.7783209371645174 chr15 102531392 79303532 0.7734561138114656 1.7817253992029398 chr16 90354753 83018278 0.9188036627137921 4.044996890794186 chr17 81195210 62967939 0.7755129766891421 2.1153908594357023 chr18 78077248 68706396 0.8799797349414774 4.047183213005841 chr19 59128983 53998411 0.9132308431552086 3.061386165045384 chr20 63025520 64269008 1.0197299125814432 2.1689875609804554 chr21 48129895 34117217 0.7088570835236603 2.9773954734888664 chr22 51304566 33833405 0.6594618693392709 1.767291602268899 chrMT 16571 3503216 211.40643292498945 176.92737798655708 chrX 155270560 147600254 0.9506003842582909 2.100282200127643 chrY 59373566 5245184 0.08834207465322194 2.8493354934346673