BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238598.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 = 3,632,413 number of mapped reads = 3,029,402 (83.4%) number of supplementary alignments = 28,806 (0.79%) number of secondary alignments = 0 number of mapped bases = 182,799,668 bp number of sequenced bases = 182,681,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,378,740 duplication rate = 22.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.1657 >>>>>>> ACTG content number of A's = 44,414,807 bp (24.31%) number of C's = 31,244,734 bp (17.1%) number of T's = 62,885,315 bp (34.42%) number of G's = 44,132,413 bp (24.16%) number of N's = 3,832 bp (0%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,186,678 number of insertions = 12,411 mapped reads with insertion percentage = 0.41% number of deletions = 70,420 mapped reads with deletion percentage = 2.3% homopolymer indels = 39.62% >>>>>>> Coverage mean coverageData = 0.059X std coverageData = 1.4562X There is a 1.45% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 9793081 0.039290096693480256 1.5518053521496318 chr2 243199373 36134907 0.1485814151338293 3.367363620355958 chr3 198022430 9740616 0.049189457982108394 0.7198942978466366 chr4 191154276 20218294 0.10576950944063632 1.3349099404223905 chr5 180915260 4479134 0.02475818789415553 0.5016889973128548 chr6 171115067 4690230 0.027409801382364533 1.076977732508418 chr7 159138663 10928764 0.06867447415968299 0.9766409620473799 chr8 146364022 7149722 0.04884890359189501 0.8655684202028174 chr9 141213431 1833379 0.012983035586749535 0.3698213384937325 chr10 135534747 2907103 0.021449134368473052 0.4713608075776765 chr11 135006516 4614413 0.034179187321595646 0.5727892085361095 chr12 133851895 2406115 0.017975950209744882 0.4203558185715788 chr13 115169878 7682553 0.06670627019332259 1.0763539735952505 chr14 107349540 2309680 0.02151550905574444 0.4529333536268454 chr15 102531392 5119497 0.04993102015039452 0.9243299367461094 chr16 90354753 15665631 0.17337915803942267 1.380820333818339 chr17 81195210 8248309 0.10158615268068154 1.0616691290525655 chr18 78077248 12442897 0.15936649047876278 4.257190663552725 chr19 59128983 8680429 0.14680497718014193 1.4637099917209535 chr20 63025520 1842599 0.029235760371354332 0.5247692523024273 chr21 48129895 2066427 0.04293437581777396 0.6666184129876866 chr22 51304566 765760 0.014925767036017808 0.3489931750972586 chrMT 16571 68372 4.126003258704967 6.783570147599828 chrX 155270560 2591370 0.016689384001706442 0.3711235833435184 chrY 59373566 420386 0.007080356264941203 0.5395522630936922