BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716969.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 = 1,888,705 number of mapped reads = 1,579,567 (83.63%) number of supplementary alignments = 3,856 (0.2%) number of secondary alignments = 0 number of mapped bases = 86,479,154 bp number of sequenced bases = 86,458,188 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,792 duplication rate = 1.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.087 >>>>>>> ACTG content number of A's = 19,893,673 bp (23.01%) number of C's = 19,694,895 bp (22.78%) number of T's = 25,399,259 bp (29.38%) number of G's = 21,468,135 bp (24.83%) number of N's = 2,226 bp (0%) GC percentage = 47.61% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 441,933 number of insertions = 5,696 mapped reads with insertion percentage = 0.36% number of deletions = 13,107 mapped reads with deletion percentage = 0.82% homopolymer indels = 36.97% >>>>>>> Coverage mean coverageData = 0.0279X std coverageData = 0.2127X There is a 2.49% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 7009638 0.028122850694923644 0.2278405780368156 chr2 243199373 7089342 0.029150330087405283 0.26014118560908794 chr3 198022430 5565778 0.028106805880525755 0.19114142362288428 chr4 191154276 5281527 0.0276296565816817 0.20314818666316284 chr5 180915260 4994435 0.027606488253119166 0.18366645990290245 chr6 171115067 4900705 0.028639821647032403 0.19246489921492296 chr7 159138663 4848452 0.030466838847326497 0.26325572791231566 chr8 146364022 4313603 0.029471744087491664 0.20153649538829135 chr9 141213431 3602191 0.025508841294281704 0.19565572110188803 chr10 135534747 4125757 0.030440585099553844 0.251184743611626 chr11 135006516 3926561 0.02908423323804608 0.23476754445886877 chr12 133851895 3951346 0.029520284341136897 0.19227339241461783 chr13 115169878 2609483 0.022657686587112646 0.16764954420380468 chr14 107349540 2642930 0.024619853983538262 0.18029513219518695 chr15 102531392 2487365 0.024259545798422398 0.17786426585906034 chr16 90354753 2839310 0.03142402481029415 0.21046546879438835 chr17 81195210 2761585 0.03401167384135099 0.21202741017238763 chr18 78077248 2214349 0.028361002170568306 0.25922733775202716 chr19 59128983 2201363 0.03722984716310781 0.24467168923103974 chr20 63025520 1934134 0.030688108563007493 0.200145399327719 chr21 48129895 1110662 0.023076343715273014 0.18645434577169082 chr22 51304566 1215207 0.023686137409290237 0.17607435747337494 chrMT 16571 8074 0.48723673888117797 0.7891607553591984 chrX 155270560 4573333 0.02945396087964132 0.2063860568279052 chrY 59373566 272024 0.004581567494194302 0.12292343014264938