BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716534.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 = 1,789,513 number of mapped reads = 1,658,614 (92.69%) number of supplementary alignments = 34,031 (1.9%) number of secondary alignments = 0 number of mapped bases = 130,414,908 bp number of sequenced bases = 130,355,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,754 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.187 >>>>>>> ACTG content number of A's = 34,238,941 bp (26.27%) number of C's = 26,194,430 bp (20.09%) number of T's = 39,449,302 bp (30.26%) number of G's = 30,462,935 bp (23.37%) number of N's = 9,429 bp (0.01%) GC percentage = 43.46% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 873,260 number of insertions = 10,453 mapped reads with insertion percentage = 0.62% number of deletions = 31,447 mapped reads with deletion percentage = 1.86% homopolymer indels = 42.53% >>>>>>> Coverage mean coverageData = 0.0421X std coverageData = 0.4091X There is a 3.63% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 12942890 0.05192721265075605 0.8816300459800381 chr2 243199373 10697409 0.04398617014526596 0.4255676563353909 chr3 198022430 8360447 0.04221969703129085 0.23044140124938164 chr4 191154276 8248833 0.043152751654898895 0.2799401848613019 chr5 180915260 7190267 0.03974383918747374 0.22376055255979035 chr6 171115067 7211287 0.042142910770096007 0.2541101073994288 chr7 159138663 6798042 0.04271772724394449 0.4838975858435243 chr8 146364022 6501766 0.044421886684693594 0.44259319238902656 chr9 141213431 5269000 0.037312314860475274 0.3275586151359941 chr10 135534747 6147872 0.045360117136604095 0.4007407323276168 chr11 135006516 6862058 0.05082760598014395 0.4439769623305964 chr12 133851895 5688094 0.04249543123763769 0.23038347253298683 chr13 115169878 4660817 0.040469062579019145 0.22504441801156946 chr14 107349540 3852934 0.03589148123038068 0.23129981139065972 chr15 102531392 3603503 0.035145363090359684 0.20786529305937007 chr16 90354753 2985248 0.033039191640532733 0.22135096186235162 chr17 81195210 4067498 0.05009529503033492 0.30017421342301887 chr18 78077248 3398159 0.04352303759476769 0.5671107211237193 chr19 59128983 2495469 0.04220382075571975 0.6069546240149896 chr20 63025520 2646085 0.04198434221566121 0.24000015317950785 chr21 48129895 1730031 0.035945039979829584 0.24528052245255422 chr22 51304566 1497735 0.029193015685972278 0.19059463833195678 chrMT 16571 5963 0.3598455132460322 0.6805682080315171 chrX 155270560 7168396 0.046167129171170634 0.28435364536081165 chrY 59373566 385105 0.006486135597784375 0.20430128063607847