BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173874.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,694,584 number of mapped reads = 2,623,346 (97.36%) number of supplementary alignments = 253,744 (9.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,312,890 number of mapped paired reads (second in pair) = 1,310,456 number of mapped paired reads (both in pair) = 2,575,398 number of mapped paired reads (singletons) = 47,948 number of mapped bases = 309,853,532 bp number of sequenced bases = 309,686,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,958,775 duplication rate = 63.69% >>>>>>> Insert size mean insert size = 875,572.9867 std insert size = 8,627,120.3204 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 52.6526 >>>>>>> ACTG content number of A's = 93,025,985 bp (30.04%) number of C's = 60,781,465 bp (19.63%) number of T's = 92,894,552 bp (30%) number of G's = 62,980,309 bp (20.34%) number of N's = 3,940 bp (0%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 3,174,625 number of insertions = 31,673 mapped reads with insertion percentage = 1.17% number of deletions = 68,905 mapped reads with deletion percentage = 2.56% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.1001X std coverageData = 1.5928X There is a 2.33% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 1.35% of reference with a coverageData >= 3X There is a 1.08% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% 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 0.02% 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% 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 22861310 0.09172017268514648 1.0581654254812314 chr2 243199373 28458226 0.11701603358985634 4.612252250742238 chr3 198022430 28513541 0.14399147106719173 1.0393904730403432 chr4 191154276 13701773 0.07167913418792682 0.7989701090226852 chr5 180915260 21448644 0.11855630088915661 0.9303421552961695 chr6 171115067 14670958 0.08573738278698742 0.8532201494072689 chr7 159138663 17950396 0.11279720252519654 1.13879541452753 chr8 146364022 15961338 0.10905233254658717 1.0909882988071335 chr9 141213431 11804852 0.08359581603820673 0.9128250118364098 chr10 135534747 15785226 0.11646626676478763 1.3121546294421027 chr11 135006516 11428545 0.08465180302852938 0.7884870200909374 chr12 133851895 15199963 0.11355807103067163 0.9103282149264497 chr13 115169878 8104918 0.07037359195604947 0.7206680237998967 chr14 107349540 10132376 0.09438676681800406 0.8276495910642784 chr15 102531392 7794038 0.07601611416725913 0.7453156746117457 chr16 90354753 10947577 0.12116215956010637 1.0810772387342387 chr17 81195210 13173619 0.16224625812286217 1.1428371311324148 chr18 78077248 6371099 0.08159994317422663 1.089124735179868 chr19 59128983 4211417 0.07122424209460866 0.8703045843031219 chr20 63025520 13530349 0.21468048181117744 1.3193459385821407 chr21 48129895 4112051 0.08543652546925357 0.7986011331832502 chr22 51304566 2238071 0.04362323228696643 0.5376988489332168 chrMT 16571 882532 53.25761873151892 44.83762546934268 chrX 155270560 10041397 0.06467032127661548 0.6793802823463467 chrY 59373566 529316 0.008915011101068107 0.37189603528881854