BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472741.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,611,164 number of mapped reads = 19,432,207 (99.09%) number of supplementary alignments = 69,229 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,749,106 number of mapped paired reads (second in pair) = 9,683,101 number of mapped paired reads (both in pair) = 19,322,998 number of mapped paired reads (singletons) = 109,209 number of mapped bases = 1,915,807,017 bp number of sequenced bases = 1,915,550,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,793,218 duplication rate = 46.97% >>>>>>> Insert size mean insert size = 22,195.5448 std insert size = 1,466,618.4527 median insert size = 251 >>>>>>> Mapping quality mean mapping quality = 55.1909 >>>>>>> ACTG content number of A's = 522,456,563 bp (27.27%) number of C's = 437,381,680 bp (22.83%) number of T's = 518,424,261 bp (27.06%) number of G's = 436,917,901 bp (22.81%) number of N's = 370,375 bp (0.02%) GC percentage = 45.64% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 11,834,476 number of insertions = 118,929 mapped reads with insertion percentage = 0.6% number of deletions = 99,745 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.19% >>>>>>> Coverage mean coverageData = 0.6189X std coverageData = 25.8315X There is a 5.19% of reference with a coverageData >= 1X There is a 2.22% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 217175334 0.8713131109912059 33.874279640338585 chr2 243199373 129802799 0.5337299903318419 25.314216182922017 chr3 198022430 155031809 0.7829002451893959 15.891368752661698 chr4 191154276 70521359 0.36892378489090144 13.911883588833742 chr5 180915260 93291085 0.5156617799957837 15.45369582190912 chr6 171115067 154106748 0.9006030310586267 31.429043133087855 chr7 159138663 91817798 0.5769672577932868 19.600459983935885 chr8 146364022 75417425 0.5152729746658643 16.99195514385044 chr9 141213431 143503528 1.0162172746868532 35.478570596445174 chr10 135534747 36895268 0.27221999388835694 9.781130900472267 chr11 135006516 94045902 0.69660268842135 26.975236214090543 chr12 133851895 135036648 1.0088512232120435 36.75985747852477 chr13 115169878 46745893 0.40588645062209755 18.349392902445505 chr14 107349540 42393186 0.3949079427820557 14.461295318757857 chr15 102531392 36023881 0.35134489347418596 11.148780685508628 chr16 90354753 66730893 0.7385432507352435 21.874210076890332 chr17 81195210 67286575 0.8287012866892025 20.87487841983173 chr18 78077248 31197710 0.39957491841925574 14.251634721863946 chr19 59128983 32102804 0.5429283977368594 13.71012638461154 chr20 63025520 36961717 0.5864563592652627 18.508819722968646 chr21 48129895 7401829 0.15378859646379864 7.549427790821858 chr22 51304566 17154144 0.33435901202243873 9.197831211829312 chrMT 16571 2641 0.15937481141753665 0.5349467937250649 chrX 155270560 128414833 0.8270391566823743 58.96455325594788 chrY 59373566 6745208 0.11360624692813634 7.203591025975538