BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716294.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 = 1,380,266 number of mapped reads = 1,292,229 (93.62%) number of supplementary alignments = 26,327 (1.91%) number of secondary alignments = 0 number of mapped bases = 99,967,018 bp number of sequenced bases = 99,928,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,822 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8833 >>>>>>> ACTG content number of A's = 25,167,181 bp (25.19%) number of C's = 20,900,704 bp (20.92%) number of T's = 29,504,445 bp (29.53%) number of G's = 24,351,834 bp (24.37%) number of N's = 4,069 bp (0%) GC percentage = 45.29% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 657,995 number of insertions = 8,513 mapped reads with insertion percentage = 0.65% number of deletions = 18,678 mapped reads with deletion percentage = 1.42% homopolymer indels = 38.64% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 0.2572X There is a 2.78% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 8932285 0.03583656066397524 0.31939670097592976 chr2 243199373 8695752 0.035755651393065066 0.30218113545848185 chr3 198022430 7071261 0.03570939413277577 0.21359149054669369 chr4 191154276 5299216 0.027722194401761643 0.2416183043185207 chr5 180915260 4452575 0.024611384357516333 0.17627189745024574 chr6 171115067 6109000 0.035701122683720186 0.22129615914019957 chr7 159138663 5951801 0.037400094281299825 0.34066779471968656 chr8 146364022 5493269 0.037531552665312794 0.29147047515836083 chr9 141213431 3189314 0.022585061331736923 0.22729858693809293 chr10 135534747 5331549 0.03933713765666305 0.32534066238281917 chr11 135006516 4946868 0.03664169809403866 0.2869098546387517 chr12 133851895 4895109 0.036571084779935314 0.21793183551000536 chr13 115169878 1760129 0.015282893674681152 0.1392325829482274 chr14 107349540 3113909 0.02900719462794158 0.2085788196870997 chr15 102531392 2903346 0.028316654473978076 0.1901800217035597 chr16 90354753 3201379 0.0354312185436443 0.22688289174058407 chr17 81195210 3069750 0.03780703319814063 0.24353492488857742 chr18 78077248 2150588 0.027544362219324124 0.34880753992498303 chr19 59128983 1806617 0.030553831781615456 0.26975615103020106 chr20 63025520 2470353 0.039196074859834555 0.23439591142080815 chr21 48129895 1435231 0.029819948703399414 0.22689898638473346 chr22 51304566 1473863 0.028727715969763784 0.20098876739442 chrMT 16571 6245 0.37686319473779495 0.6394343679820779 chrX 155270560 5870691 0.037809427621050634 0.23285150448162287 chrY 59373566 336918 0.005674545470285548 0.20259296470832777