BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124853.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 = 113,104,862 number of mapped reads = 109,101,875 (96.46%) number of supplementary alignments = 2,912,929 (2.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 55,010,160 number of mapped paired reads (second in pair) = 54,091,715 number of mapped paired reads (both in pair) = 107,916,754 number of mapped paired reads (singletons) = 1,185,121 number of mapped bases = 14,301,668,695 bp number of sequenced bases = 14,289,794,187 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,547,865 duplication rate = 23.93% >>>>>>> Insert size mean insert size = 141,329.8137 std insert size = 3,527,034.0985 median insert size = 252 >>>>>>> Mapping quality mean mapping quality = 53.1832 >>>>>>> ACTG content number of A's = 4,098,621,518 bp (28.68%) number of C's = 2,751,616,658 bp (19.26%) number of T's = 4,258,991,491 bp (29.8%) number of G's = 3,180,243,183 bp (22.26%) number of N's = 321,337 bp (0%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 172,502,333 number of insertions = 2,983,352 mapped reads with insertion percentage = 2.52% number of deletions = 5,147,527 mapped reads with deletion percentage = 4.49% homopolymer indels = 43.96% >>>>>>> Coverage mean coverageData = 4.6199X std coverageData = 76.3668X There is a 57.22% of reference with a coverageData >= 1X There is a 45.2% of reference with a coverageData >= 2X There is a 37.03% of reference with a coverageData >= 3X There is a 31.24% of reference with a coverageData >= 4X There is a 26.64% of reference with a coverageData >= 5X There is a 22.97% of reference with a coverageData >= 6X There is a 19.96% of reference with a coverageData >= 7X There is a 17.46% of reference with a coverageData >= 8X There is a 15.35% of reference with a coverageData >= 9X There is a 13.56% of reference with a coverageData >= 10X There is a 12.03% of reference with a coverageData >= 11X There is a 10.72% of reference with a coverageData >= 12X There is a 9.57% of reference with a coverageData >= 13X There is a 8.58% of reference with a coverageData >= 14X There is a 7.72% of reference with a coverageData >= 15X There is a 6.96% of reference with a coverageData >= 16X There is a 6.28% of reference with a coverageData >= 17X There is a 5.69% of reference with a coverageData >= 18X There is a 5.16% of reference with a coverageData >= 19X There is a 4.7% of reference with a coverageData >= 20X There is a 4.28% of reference with a coverageData >= 21X There is a 3.9% of reference with a coverageData >= 22X There is a 3.57% of reference with a coverageData >= 23X There is a 3.27% of reference with a coverageData >= 24X There is a 3% of reference with a coverageData >= 25X There is a 2.75% of reference with a coverageData >= 26X There is a 2.53% of reference with a coverageData >= 27X There is a 2.33% of reference with a coverageData >= 28X There is a 2.15% of reference with a coverageData >= 29X There is a 1.98% of reference with a coverageData >= 30X There is a 1.83% of reference with a coverageData >= 31X There is a 1.7% of reference with a coverageData >= 32X There is a 1.57% of reference with a coverageData >= 33X There is a 1.46% of reference with a coverageData >= 34X There is a 1.35% of reference with a coverageData >= 35X There is a 1.26% of reference with a coverageData >= 36X There is a 1.17% of reference with a coverageData >= 37X There is a 1.09% of reference with a coverageData >= 38X There is a 1.01% of reference with a coverageData >= 39X There is a 0.95% of reference with a coverageData >= 40X There is a 0.88% of reference with a coverageData >= 41X There is a 0.83% of reference with a coverageData >= 42X There is a 0.77% of reference with a coverageData >= 43X There is a 0.72% of reference with a coverageData >= 44X There is a 0.68% of reference with a coverageData >= 45X There is a 0.64% of reference with a coverageData >= 46X There is a 0.6% of reference with a coverageData >= 47X There is a 0.56% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.5% of reference with a coverageData >= 50X There is a 0.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1213654328 4.869212855441591 65.62079396206379 chr2 243199373 1179643403 4.850519918897982 73.63878094695355 chr3 198022430 986064692 4.979560608361386 10.65756464463335 chr4 191154276 766091871 4.007715061524441 90.24841048862345 chr5 180915260 772468732 4.269782062607654 10.268994313706488 chr6 171115067 816388780 4.770992959959511 30.371266858301205 chr7 159138663 982638980 6.174734420132712 57.33161245935816 chr8 146364022 952798422 6.509785731359583 20.895772525210432 chr9 141213431 536144341 3.7966950962334454 86.82929325722148 chr10 135534747 782258589 5.7716460635736455 250.3377370956709 chr11 135006516 481245074 3.564606274263088 21.904927207373778 chr12 133851895 656743206 4.906491656319098 23.55831680850248 chr13 115169878 317242868 2.7545645919673545 6.0573647461679405 chr14 107349540 578002445 5.384302950902258 11.953676077990073 chr15 102531392 358916597 3.5005532451953836 13.067197942791385 chr16 90354753 542381917 6.002804489986265 113.37784584959462 chr17 81195210 302707019 3.7281388766652612 59.1178614013124 chr18 78077248 229426748 2.938458435420265 68.25261517385707 chr19 59128983 220226101 3.724503446981322 34.013216027916236 chr20 63025520 314999935 4.99797439196059 28.466165209618982 chr21 48129895 153660298 3.192616522433718 43.801979841917515 chr22 51304566 107991793 2.1049158275698114 8.487011730607124 chrMT 16571 17469750 1054.2363164564601 508.60456371440534 chrX 155270560 693002207 4.463191264332401 15.588076353690472 chrY 59373566 339500599 5.7180429250282865 158.72912758546565