BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234149.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 = 1,008,614 number of mapped reads = 642,952 (63.75%) number of supplementary alignments = 6,773 (0.67%) number of secondary alignments = 0 number of mapped bases = 42,471,502 bp number of sequenced bases = 42,450,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,579 duplication rate = 6.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0378 >>>>>>> ACTG content number of A's = 12,131,275 bp (28.58%) number of C's = 7,342,901 bp (17.3%) number of T's = 14,034,138 bp (33.06%) number of G's = 8,934,361 bp (21.05%) number of N's = 8,172 bp (0.02%) GC percentage = 38.34% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 341,341 number of insertions = 3,769 mapped reads with insertion percentage = 0.58% number of deletions = 11,485 mapped reads with deletion percentage = 1.76% homopolymer indels = 44.9% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 0.2079X There is a 0.96% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 2656078 0.010656254292742565 0.2811760852065853 chr2 243199373 3736187 0.015362650626570488 0.2037652908763497 chr3 198022430 3093384 0.015621381880830369 0.16961686344006682 chr4 191154276 3410574 0.017841996900974374 0.18611320739084197 chr5 180915260 2599067 0.014366212114997928 0.16227200088201546 chr6 171115067 2565931 0.014995353974293801 0.17451175325283672 chr7 159138663 2091085 0.013140018651532847 0.17886235381506926 chr8 146364022 2849516 0.019468691561372917 0.44235962335897944 chr9 141213431 1709442 0.012105378276659817 0.2136393203408754 chr10 135534747 2247414 0.01658182901245243 0.20578121568446445 chr11 135006516 1805692 0.013374850736834065 0.17211740892398614 chr12 133851895 1808444 0.013510783691183453 0.1586965215364058 chr13 115169878 1593387 0.013835101917881688 0.15966334996167364 chr14 107349540 1401405 0.013054597159894677 0.15759930325506677 chr15 102531392 1010894 0.00985936092626149 0.13163476409897804 chr16 90354753 994124 0.011002453849882141 0.14150792573982654 chr17 81195210 881037 0.010850849452818707 0.14255611042486285 chr18 78077248 1232972 0.015791693887571446 0.2802800766850172 chr19 59128983 625059 0.010571110279370102 0.2081693298911196 chr20 63025520 951945 0.01510411972800859 0.16608802708739945 chr21 48129895 578178 0.012012866431559844 0.14967804949169755 chr22 51304566 323103 0.006297743557561719 0.10293210381394516 chrMT 16571 102557 6.188944541669181 5.12424462277988 chrX 155270560 2063898 0.01329226866960485 0.16087084187870374 chrY 59373566 140129 0.00236012436915108 0.07949533232662755