BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038401.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 12,319,864 number of mapped reads = 12,012,975 (97.51%) number of supplementary alignments = 234,565 (1.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,089,712 number of mapped paired reads (second in pair) = 5,923,263 number of mapped paired reads (both in pair) = 11,829,098 number of mapped paired reads (singletons) = 183,877 number of mapped bases = 1,719,191,827 bp number of sequenced bases = 1,717,959,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,753,402 duplication rate = 7.59% >>>>>>> Insert size mean insert size = 103,672.5029 std insert size = 3,028,492.466 median insert size = 271 >>>>>>> Mapping quality mean mapping quality = 53.6324 >>>>>>> ACTG content number of A's = 500,003,338 bp (29.1%) number of C's = 353,474,575 bp (20.58%) number of T's = 501,100,842 bp (29.17%) number of G's = 363,345,262 bp (21.15%) number of N's = 35,955 bp (0%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 27,034,965 number of insertions = 317,664 mapped reads with insertion percentage = 2.46% number of deletions = 586,723 mapped reads with deletion percentage = 4.68% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.5553X std coverageData = 9.6549X There is a 26.24% of reference with a coverageData >= 1X There is a 12.22% of reference with a coverageData >= 2X There is a 5.64% of reference with a coverageData >= 3X There is a 2.91% of reference with a coverageData >= 4X There is a 1.51% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% 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 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 103987402 0.4172001721913463 11.092941875262339 chr2 243199373 171676109 0.7059068733701053 13.076426276504113 chr3 198022430 113460708 0.5729689712422982 1.2393650340016982 chr4 191154276 101961444 0.5333987088000062 8.95913009308672 chr5 180915260 100632484 0.5562409937116416 1.3394193362479099 chr6 171115067 118237151 0.6909803623546488 14.217695125277903 chr7 159138663 109688752 0.6892652604477392 10.120098908758436 chr8 146364022 78307945 0.5350218170418957 2.7321340127556426 chr9 141213431 70750094 0.5010153318914827 16.379977308031236 chr10 135534747 82877220 0.611483194047649 18.87232971921548 chr11 135006516 85505521 0.6333436602422953 6.6155289459934865 chr12 133851895 55385255 0.41378013363202665 1.067830888615691 chr13 115169878 111805381 0.9707866582961909 1.7679493888331947 chr14 107349540 30971911 0.28851461310407106 1.055106333350041 chr15 102531392 29186495 0.28465911201127553 0.7976382978090297 chr16 90354753 67927248 0.7517838934272777 15.150218781837678 chr17 81195210 36552543 0.45018102668864335 7.12174120300617 chr18 78077248 31154201 0.3990176626102395 13.784474671981254 chr19 59128983 20869427 0.3529475046103871 6.568111582450267 chr20 63025520 57216444 0.9078297806983584 2.8987308679527164 chr21 48129895 14865555 0.30886323354746564 4.0023503737604855 chr22 51304566 9422052 0.18364938512490292 0.7970932373738393 chrMT 16571 1085414 65.50081467624163 38.995959911647304 chrX 155270560 85211491 0.5487936090396016 1.9511376106442953 chrY 59373566 30453580 0.5129147877019885 13.764375139780947