BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716594.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 = 1,603,767 number of mapped reads = 1,474,432 (91.94%) number of supplementary alignments = 4,529 (0.28%) number of secondary alignments = 0 number of mapped bases = 85,460,603 bp number of sequenced bases = 85,433,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,939 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0233 >>>>>>> ACTG content number of A's = 20,946,344 bp (24.52%) number of C's = 16,001,948 bp (18.73%) number of T's = 27,475,887 bp (32.16%) number of G's = 21,008,673 bp (24.59%) number of N's = 776 bp (0%) GC percentage = 43.32% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 417,745 number of insertions = 6,371 mapped reads with insertion percentage = 0.43% number of deletions = 16,470 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.79% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 0.2404X There is a 2.47% 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 6814774 0.027341051238544356 0.3190234060441855 chr2 243199373 7235399 0.029750894958105012 0.3374914446199544 chr3 198022430 5664289 0.028604279828300258 0.18564289005355922 chr4 191154276 5469318 0.028612062018429554 0.2037287875174896 chr5 180915260 5165545 0.028552290171652738 0.18465321143865648 chr6 171115067 4930462 0.02881372217211007 0.218019913346325 chr7 159138663 4677547 0.02939290120842601 0.34209883692750803 chr8 146364022 4268866 0.0291660883710889 0.2405874302195196 chr9 141213431 3532089 0.025012415426688413 0.20778730252106908 chr10 135534747 4118306 0.030385610267159018 0.26927186111303525 chr11 135006516 3866114 0.0286364992931156 0.2250073612255633 chr12 133851895 3878186 0.028973710084567724 0.1872510194234789 chr13 115169878 2702918 0.023468966425405087 0.16770712302120705 chr14 107349540 2593802 0.024162208799404263 0.17488714848709672 chr15 102531392 2477600 0.024164306673998926 0.1706782232757778 chr16 90354753 2596962 0.028741841616234623 0.20029601450178 chr17 81195210 2395601 0.029504215827510023 0.2014826266130285 chr18 78077248 2266536 0.02902940431507012 0.33394574884380873 chr19 59128983 1813770 0.030674804604706292 0.27334474964190036 chr20 63025520 1834185 0.029102258894492264 0.19162583726359597 chr21 48129895 1115915 0.023185485860710894 0.18222386723052303 chr22 51304566 1040528 0.02028139171862403 0.155743293513138 chrMT 16571 15109 0.911773580351216 1.0354005845832794 chrX 155270560 4729681 0.03046089999288983 0.20590595546896057 chrY 59373566 257101 0.0043302266870748505 0.12415468800440102