BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230337.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,686,307 number of mapped reads = 2,202,868 (82%) number of supplementary alignments = 11,501 (0.43%) number of secondary alignments = 0 number of mapped bases = 141,081,910 bp number of sequenced bases = 141,016,395 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,643 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1487 >>>>>>> ACTG content number of A's = 37,280,985 bp (26.44%) number of C's = 23,761,838 bp (16.85%) number of T's = 47,109,192 bp (33.41%) number of G's = 32,604,759 bp (23.12%) number of N's = 259,621 bp (0.18%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,338,224 number of insertions = 13,147 mapped reads with insertion percentage = 0.59% number of deletions = 40,776 mapped reads with deletion percentage = 1.83% homopolymer indels = 49% >>>>>>> Coverage mean coverageData = 0.0456X std coverageData = 0.4864X There is a 3.93% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 12213247 0.048999865881979084 0.7919342122948463 chr2 243199373 12295113 0.050555693661266145 0.5139831283208616 chr3 198022430 7554645 0.0381504509362904 0.2176506996332343 chr4 191154276 10984105 0.057461989497948764 0.31135276455242317 chr5 180915260 7893222 0.04362938759284319 0.23751765933756455 chr6 171115067 8294209 0.04847152939489542 0.33831154438948685 chr7 159138663 7434095 0.04671457494901789 0.603645878742621 chr8 146364022 6968605 0.04761146151067098 1.081346804990545 chr9 141213431 6311845 0.044697200225947344 0.494209294000113 chr10 135534747 6803489 0.05019737853644276 0.3637166365435628 chr11 135006516 6547672 0.048498933192231995 0.48092496050945793 chr12 133851895 5875870 0.04389829520157335 0.24257616903549264 chr13 115169878 5137221 0.04460559557074464 0.23546806537118278 chr14 107349540 5022574 0.04678710313989236 0.2651956520354853 chr15 102531392 3762661 0.0366976486576911 0.21578539840054375 chr16 90354753 4220557 0.046710957197791246 0.27710224873798495 chr17 81195210 2707944 0.03335103142168116 0.2753677524514039 chr18 78077248 4173817 0.05345753221220092 0.8717486024694826 chr19 59128983 2380723 0.0402632157566451 0.49930392844575205 chr20 63025520 2821807 0.04477245090560141 0.25810563684838084 chr21 48129895 2162754 0.04493577224716572 0.26588256055450404 chr22 51304566 1482214 0.028890489006378108 0.18696386402616558 chrMT 16571 128540 7.756924748053829 4.984853179642314 chrX 155270560 7508337 0.04835647530349604 0.3109227682103667 chrY 59373566 396644 0.00668048134417259 0.15900812919499843