BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231887.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 = 5,842,121 number of mapped reads = 5,416,718 (92.72%) number of supplementary alignments = 38,617 (0.66%) number of secondary alignments = 0 number of mapped bases = 368,483,185 bp number of sequenced bases = 368,346,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 501,874 duplication rate = 4.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1003 >>>>>>> ACTG content number of A's = 98,255,248 bp (26.67%) number of C's = 67,978,647 bp (18.46%) number of T's = 108,096,038 bp (29.35%) number of G's = 93,937,066 bp (25.5%) number of N's = 79,443 bp (0.02%) GC percentage = 43.96% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 2,454,206 number of insertions = 25,475 mapped reads with insertion percentage = 0.47% number of deletions = 83,992 mapped reads with deletion percentage = 1.54% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.119X std coverageData = 28.1802X There is a 8.13% of reference with a coverageData >= 1X There is a 2.12% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 36634985 0.14698051644974638 2.2804879066331503 chr2 243199373 40595099 0.1669210676789039 100.48229051806806 chr3 198022430 23327240 0.11780099860404702 0.45555655179020876 chr4 191154276 19426819 0.10162900567288383 0.45582855761454033 chr5 180915260 23649258 0.13072008408798683 0.49648035591752077 chr6 171115067 26214614 0.15319874783440315 0.672524915539582 chr7 159138663 16466738 0.10347415071597026 1.2194951986008367 chr8 146364022 20498279 0.14004998441488578 1.0515524196399748 chr9 141213431 15073819 0.10674493844710847 0.9151634830256603 chr10 135534747 14411560 0.10633110932062315 0.6908977021435982 chr11 135006516 13221249 0.09793045100134277 0.8602075466719437 chr12 133851895 9688891 0.07238516122614476 0.39763770302950585 chr13 115169878 11945455 0.10372030610295514 0.4262056476444214 chr14 107349540 14540089 0.13544621616450336 0.7009592492000961 chr15 102531392 12296993 0.11993393203907736 0.46761239731041965 chr16 90354753 10902653 0.1206649638010742 0.5784333163224079 chr17 81195210 9427134 0.11610455838466333 0.5832258481895316 chr18 78077248 11337588 0.14520988239749433 1.910577279432716 chr19 59128983 8528406 0.14423393684954805 1.513953624518408 chr20 63025520 7751959 0.12299714464870738 0.5170991824566348 chr21 48129895 8222714 0.17084421231336575 0.6288236730467767 chr22 51304566 2805832 0.054689713192389154 0.30481420243716373 chrMT 16571 35052 2.1152616015931445 2.283996280844119 chrX 155270560 10674343 0.06874672829157054 0.49362583009091837 chrY 59373566 806416 0.013582071186359262 0.25835815697295006