BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716257.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,049,643 number of mapped reads = 994,954 (94.79%) number of supplementary alignments = 20,569 (1.96%) number of secondary alignments = 0 number of mapped bases = 77,260,824 bp number of sequenced bases = 77,229,868 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,826 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8906 >>>>>>> ACTG content number of A's = 19,797,847 bp (25.63%) number of C's = 15,471,797 bp (20.03%) number of T's = 22,691,470 bp (29.38%) number of G's = 19,265,877 bp (24.95%) number of N's = 2,877 bp (0%) GC percentage = 44.98% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 473,112 number of insertions = 5,901 mapped reads with insertion percentage = 0.58% number of deletions = 14,918 mapped reads with deletion percentage = 1.48% homopolymer indels = 38.99% >>>>>>> Coverage mean coverageData = 0.025X std coverageData = 0.229X There is a 2.21% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8523546 0.0341966891227926 0.4106641478462612 chr2 243199373 7395491 0.03040916968153532 0.24758809506356072 chr3 198022430 5038591 0.025444546862696312 0.17723152217546476 chr4 191154276 3776366 0.019755592597886746 0.19694135686398723 chr5 180915260 3970271 0.021945473256374283 0.16353185248998442 chr6 171115067 4379321 0.025592842738974 0.1823584794488116 chr7 159138663 4942335 0.03105678347944899 0.28576003646565584 chr8 146364022 4859315 0.03320020134456267 0.25011767887590314 chr9 141213431 2320791 0.016434633614985247 0.16632959392837185 chr10 135534747 3199980 0.023610034111769138 0.28430198287042624 chr11 135006516 3306074 0.024488255070592296 0.2077813322882041 chr12 133851895 3104057 0.02319023574526158 0.16853342384555595 chr13 115169878 1495568 0.012985756570828354 0.12461463279595514 chr14 107349540 1524117 0.014197704060958249 0.13525627520125316 chr15 102531392 1587274 0.015480858779328774 0.13675046182856462 chr16 90354753 2355395 0.026068302129053464 0.182724426019471 chr17 81195210 1926399 0.023725525188000623 0.18014832946198084 chr18 78077248 2257133 0.02890897230394186 0.24044977182167704 chr19 59128983 1885649 0.03189043518641273 0.29833045032901606 chr20 63025520 2060201 0.03268836179376227 0.20395317591419648 chr21 48129895 1011646 0.021019077643946657 0.185254789810269 chr22 51304566 1176651 0.02293462535088982 0.16883948844481997 chrMT 16571 9577 0.5779373604489771 0.9154152175048134 chrX 155270560 4910736 0.03162696135056124 0.2021093025659492 chrY 59373566 244340 0.004115299390978133 0.14648261017122238