BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234101.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 = 5,321,703 number of mapped reads = 5,022,518 (94.38%) number of supplementary alignments = 31,937 (0.6%) number of secondary alignments = 0 number of mapped bases = 323,251,673 bp number of sequenced bases = 323,122,160 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 535,688 duplication rate = 8.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8337 >>>>>>> ACTG content number of A's = 83,423,882 bp (25.82%) number of C's = 58,351,796 bp (18.06%) number of T's = 104,924,977 bp (32.47%) number of G's = 76,390,903 bp (23.64%) number of N's = 30,602 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,782,642 number of insertions = 20,893 mapped reads with insertion percentage = 0.41% number of deletions = 74,170 mapped reads with deletion percentage = 1.46% homopolymer indels = 44.04% >>>>>>> Coverage mean coverageData = 0.1044X std coverageData = 1.1505X There is a 7.99% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 31378698 0.12589215575113852 2.5003526625288024 chr2 243199373 18271205 0.0751285037235684 1.9602034875892083 chr3 198022430 38695326 0.19540880293207188 0.5585625733300187 chr4 191154276 11509436 0.060210193780860025 0.385006863812516 chr5 180915260 17782465 0.09829168086760619 0.41277872810301514 chr6 171115067 22145507 0.12941880214440732 0.814551132086876 chr7 159138663 22501757 0.14139717260286397 1.6517858549669235 chr8 146364022 17947422 0.12262181480637366 1.0858842429370004 chr9 141213431 11331922 0.08024677199437212 0.702613095415045 chr10 135534747 14662524 0.10818276733124385 0.7911244632346288 chr11 135006516 12533783 0.09283835603905222 0.6701926420730457 chr12 133851895 10146146 0.07580128768442165 0.38729684874520043 chr13 115169878 13466319 0.11692570343783815 0.4951982008356128 chr14 107349540 15938189 0.14847002604761977 0.5320986834788398 chr15 102531392 6722253 0.06556287658710418 0.3925638094212849 chr16 90354753 8477806 0.09382800260657012 0.4851779357655525 chr17 81195210 8348790 0.10282367642130613 0.4733728783184164 chr18 78077248 5958342 0.07631342231734398 1.7053046493960298 chr19 59128983 9453214 0.15987445615291573 1.3983610816405865 chr20 63025520 8022650 0.1272920873957089 0.48323947311527876 chr21 48129895 5921994 0.12304190565967368 0.47345547015751865 chr22 51304566 2382098 0.046430526281033155 0.258748695352063 chrMT 16571 220676 13.316999577575283 7.975873322605105 chrX 155270560 8732102 0.05623797582748462 0.4419104680460267 chrY 59373566 701049 0.011807426220618112 0.2535091653050234