BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173912.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 = 1,617,794 number of mapped reads = 1,578,122 (97.55%) number of supplementary alignments = 161,868 (10.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 790,704 number of mapped paired reads (second in pair) = 787,418 number of mapped paired reads (both in pair) = 1,552,846 number of mapped paired reads (singletons) = 25,276 number of mapped bases = 187,413,679 bp number of sequenced bases = 187,298,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,205,513 duplication rate = 62.81% >>>>>>> Insert size mean insert size = 1,196,190.5113 std insert size = 10,109,181.5542 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 52.9375 >>>>>>> ACTG content number of A's = 56,395,187 bp (30.11%) number of C's = 36,667,086 bp (19.58%) number of T's = 56,259,140 bp (30.04%) number of G's = 37,974,946 bp (20.28%) number of N's = 2,540 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 1,971,874 number of insertions = 21,750 mapped reads with insertion percentage = 1.32% number of deletions = 44,960 mapped reads with deletion percentage = 2.78% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0605X std coverageData = 1.0045X There is a 1.37% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% 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 15531287 0.062311929004180894 0.8241677107043355 chr2 243199373 16923685 0.0695876999649995 2.4508791806471715 chr3 198022430 12635949 0.06381069558635352 0.7098688439837751 chr4 191154276 12665287 0.06625688561630712 0.8370403259167732 chr5 180915260 11252298 0.0621965112285166 0.6993809834028691 chr6 171115067 11932599 0.06973435600501504 0.7901723467338087 chr7 159138663 10659639 0.06698333892625452 0.8451029581958959 chr8 146364022 9207385 0.0629074336314699 0.85545991216655 chr9 141213431 7870008 0.055731299383271836 0.7899309674798011 chr10 135534747 9255417 0.06828814901613385 0.9876634637364835 chr11 135006516 8335207 0.06173929412414435 0.6976963486022995 chr12 133851895 8629767 0.06447250522676574 0.7190521315638921 chr13 115169878 6224058 0.05404241202721427 0.6600859091243753 chr14 107349540 5691371 0.053017190385724985 0.6438257199240465 chr15 102531392 5309570 0.051784823130071225 0.620711570264608 chr16 90354753 5836894 0.0645997449630569 0.789065824572277 chr17 81195210 5037560 0.062042576156893986 0.7379296683675859 chr18 78077248 5492726 0.07034989245522588 1.0370635746204522 chr19 59128983 3264037 0.055201981065698354 0.6922831938166716 chr20 63025520 4014613 0.06369821304132041 0.7089389248243018 chr21 48129895 2734544 0.05681591451633127 0.7823700377131776 chr22 51304566 2250839 0.04387209902526025 0.5784891284594089 chrMT 16571 258505 15.599843099390501 15.959718887912638 chrX 155270560 4837198 0.03115334935354133 0.49181331652684335 chrY 59373566 1563236 0.02632882114576039 0.5398904642915325