BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054603.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 10,252,471 number of mapped reads = 8,086,633 (78.87%) number of supplementary alignments = 292 (0%) number of secondary alignments = 0 number of mapped bases = 381,770,635 bp number of sequenced bases = 381,687,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,611,453 duplication rate = 14.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5584 >>>>>>> ACTG content number of A's = 115,997,703 bp (30.39%) number of C's = 70,843,303 bp (18.56%) number of T's = 116,855,583 bp (30.62%) number of G's = 77,843,874 bp (20.39%) number of N's = 147,238 bp (0.04%) GC percentage = 38.96% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,853,377 number of insertions = 17,228 mapped reads with insertion percentage = 0.21% number of deletions = 56,053 mapped reads with deletion percentage = 0.69% homopolymer indels = 49% >>>>>>> Coverage mean coverageData = 0.1233X std coverageData = 0.8393X There is a 5.81% of reference with a coverageData >= 1X There is a 2.36% of reference with a coverageData >= 2X There is a 1.28% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% 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 0.02% 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 0.02% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 34090728 0.13677289092892572 0.9357771052405303 chr2 243199373 31259501 0.12853446377923022 0.9067725026136639 chr3 198022430 28275673 0.14279025360914924 0.8439161804592271 chr4 191154276 24963731 0.13059467735893074 0.8407495756926977 chr5 180915260 18897615 0.1044556164029502 0.6731201847135534 chr6 171115067 19076689 0.1114845661136316 0.7742143703540814 chr7 159138663 25088174 0.15764977238749328 1.0149838850468027 chr8 146364022 19684912 0.1344928332182618 0.916659376135119 chr9 141213431 17974805 0.12728821099177173 0.8689340350918037 chr10 135534747 16156355 0.11920452398822864 0.8103720557785236 chr11 135006516 16926492 0.125375370770993 0.8327342632693445 chr12 133851895 14405945 0.10762600708790862 0.6978774987277551 chr13 115169878 12509483 0.10861766303164791 0.7083515248116301 chr14 107349540 7940068 0.0739646206215695 0.6285181754311544 chr15 102531392 9762601 0.09521572671128858 0.6479411195004044 chr16 90354753 10097332 0.11175208458596528 0.8051810228985529 chr17 81195210 6976625 0.08592409576870359 0.6000849139210047 chr18 78077248 14881890 0.19060469446873948 1.1904179681175824 chr19 59128983 6764526 0.11440288090190896 0.8317750974592035 chr20 63025520 6962799 0.11047586755333395 0.7386005137574835 chr21 48129895 4825446 0.10025881003895812 0.802393281562721 chr22 51304566 3448454 0.0672153429774652 0.5224043713714726 chrMT 16571 123277 7.439321706595861 13.860029800330167 chrX 155270560 29626585 0.19080619661576542 1.0852364684267637 chrY 59373566 1050929 0.017700284331919697 0.3756323821615008