BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173952.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 8,923,762 number of mapped reads = 8,717,814 (97.69%) number of supplementary alignments = 1,191,134 (13.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,360,251 number of mapped paired reads (second in pair) = 4,357,563 number of mapped paired reads (both in pair) = 8,587,380 number of mapped paired reads (singletons) = 130,434 number of mapped bases = 985,996,657 bp number of sequenced bases = 985,304,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,941,466 duplication rate = 64.55% >>>>>>> Insert size mean insert size = 999,851.7319 std insert size = 9,546,009.2179 median insert size = 152 >>>>>>> Mapping quality mean mapping quality = 52.5724 >>>>>>> ACTG content number of A's = 292,690,232 bp (29.71%) number of C's = 196,963,997 bp (19.99%) number of T's = 290,350,785 bp (29.47%) number of G's = 205,292,595 bp (20.84%) number of N's = 7,250 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 8,459,949 number of insertions = 104,995 mapped reads with insertion percentage = 1.16% number of deletions = 300,948 mapped reads with deletion percentage = 3.37% homopolymer indels = 41.02% >>>>>>> Coverage mean coverageData = 0.3185X std coverageData = 6.0412X There is a 6.93% of reference with a coverageData >= 1X There is a 5.2% of reference with a coverageData >= 2X There is a 3.84% of reference with a coverageData >= 3X There is a 3.08% of reference with a coverageData >= 4X There is a 2.29% of reference with a coverageData >= 5X There is a 1.9% of reference with a coverageData >= 6X There is a 1.41% of reference with a coverageData >= 7X There is a 1.22% of reference with a coverageData >= 8X There is a 0.91% of reference with a coverageData >= 9X There is a 0.82% of reference with a coverageData >= 10X There is a 0.61% of reference with a coverageData >= 11X There is a 0.56% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.38% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% 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% 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 81420656 0.3266617979659918 2.6851434991657217 chr2 243199373 85848856 0.3529978508620579 20.247522991276107 chr3 198022430 66965842 0.3381730140368442 1.7287446186378985 chr4 191154276 62481374 0.32686359576910534 2.25128466535113 chr5 180915260 68184046 0.3768838847535581 1.8293835524975002 chr6 171115067 57759874 0.33754990143562286 2.0673805394231946 chr7 159138663 57061458 0.3585643923626529 2.522941637792317 chr8 146364022 51768809 0.35369900534709275 2.6913245573581115 chr9 141213431 39710417 0.2812084992113817 2.140061801115674 chr10 135534747 46431716 0.3425816407064972 3.048972206436913 chr11 135006516 44210881 0.32747220141581906 1.7732770022986508 chr12 133851895 46661860 0.34860813886871006 1.8568522376091745 chr13 115169878 30541860 0.26518965314871656 1.545318010904683 chr14 107349540 29835774 0.2779310838220639 1.587458321325958 chr15 102531392 29481730 0.28753857160156376 1.6530242182705288 chr16 90354753 30778783 0.34064376226007725 2.2509096607809362 chr17 81195210 29676668 0.36549776766388065 1.9310837942808539 chr18 78077248 25998621 0.3329858782932513 2.773750496481482 chr19 59128983 19972413 0.3377770424361941 2.1601632141527567 chr20 63025520 22410636 0.3555803426929282 1.8179308527111608 chr21 48129895 12987359 0.26983975344222133 2.107422482875282 chr22 51304566 12757765 0.2486672433794684 1.77105406876548 chrMT 16571 1599356 96.51535815581437 78.10319142859204 chrX 155270560 24364930 0.1569191867408735 1.1958988486463453 chrY 59373566 7084973 0.11932874303018956 1.7731665503607328