BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173855.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 = 9,846,802 number of mapped reads = 9,571,475 (97.2%) number of supplementary alignments = 992,581 (10.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,796,792 number of mapped paired reads (second in pair) = 4,774,683 number of mapped paired reads (both in pair) = 9,379,702 number of mapped paired reads (singletons) = 191,773 number of mapped bases = 1,129,067,350 bp number of sequenced bases = 1,128,408,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,279,684 duplication rate = 64.1% >>>>>>> Insert size mean insert size = 929,089.5707 std insert size = 8,944,553.016 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.716 >>>>>>> ACTG content number of A's = 334,373,786 bp (29.63%) number of C's = 225,456,040 bp (19.98%) number of T's = 334,321,867 bp (29.63%) number of G's = 234,243,474 bp (20.76%) number of N's = 13,048 bp (0%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 11,694,443 number of insertions = 113,738 mapped reads with insertion percentage = 1.15% number of deletions = 274,933 mapped reads with deletion percentage = 2.8% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.3647X std coverageData = 4.9756X There is a 7.83% of reference with a coverageData >= 1X There is a 6.18% of reference with a coverageData >= 2X There is a 4.74% of reference with a coverageData >= 3X There is a 3.84% of reference with a coverageData >= 4X There is a 2.88% of reference with a coverageData >= 5X There is a 2.3% of reference with a coverageData >= 6X There is a 1.69% of reference with a coverageData >= 7X There is a 1.36% of reference with a coverageData >= 8X There is a 1% of reference with a coverageData >= 9X There is a 0.83% of reference with a coverageData >= 10X There is a 0.61% of reference with a coverageData >= 11X There is a 0.52% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% 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% 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 107395185 0.430872286572959 2.4752784188012362 chr2 243199373 84666587 0.34813653487503027 15.904486056388869 chr3 198022430 68830013 0.3475869526497579 1.6522550098793052 chr4 191154276 63192510 0.33058381597490394 2.0272541165154356 chr5 180915260 54295120 0.30011354487178143 1.5150017144898644 chr6 171115067 56634740 0.3309745950074636 1.6613242101560555 chr7 159138663 95268287 0.598649537479148 4.150599427577131 chr8 146364022 102278117 0.6987927470317808 2.9591633915473863 chr9 141213431 40665767 0.2879737905383802 1.9327719209478385 chr10 135534747 51160528 0.3774716752155077 4.215103678256177 chr11 135006516 47214920 0.3497232681717377 1.6955310676403155 chr12 133851895 44261987 0.3306788222908611 1.6129964147453204 chr13 115169878 27654261 0.2401171337526293 1.3535450715063413 chr14 107349540 39302923 0.366121019242374 1.7148074033413667 chr15 102531392 29426220 0.2869971764354862 1.4833816133519693 chr16 90354753 27707462 0.30665195886264 2.027464758374927 chr17 81195210 35403601 0.436030659936713 2.039553871895111 chr18 78077248 17506872 0.22422501366851455 2.314199089860547 chr19 59128983 17736022 0.29995479543424586 1.9231540886431433 chr20 63025520 48149318 0.763965422260697 2.5055868343135974 chr21 48129895 13624851 0.28308499322510466 1.5901085073451608 chr22 51304566 14630598 0.285171460177638 1.4383579088140537 chrMT 16571 2449085 147.79343431295638 104.60749663168089 chrX 155270560 37904158 0.24411683708746848 1.3780772582400445 chrY 59373566 1708218 0.0287706822258242 1.1265954083800935