BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716160.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 = 1,535,397 number of mapped reads = 1,247,239 (81.23%) number of supplementary alignments = 4,758 (0.31%) number of secondary alignments = 0 number of mapped bases = 70,868,119 bp number of sequenced bases = 70,848,970 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,251 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1144 >>>>>>> ACTG content number of A's = 18,035,540 bp (25.46%) number of C's = 12,563,196 bp (17.73%) number of T's = 22,190,820 bp (31.32%) number of G's = 18,057,826 bp (25.49%) number of N's = 1,588 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 348,746 number of insertions = 4,601 mapped reads with insertion percentage = 0.37% number of deletions = 11,186 mapped reads with deletion percentage = 0.89% homopolymer indels = 41.49% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 0.1936X There is a 2.1% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 8071474 0.03238296445407853 0.2753568817884552 chr2 243199373 6079627 0.02499853073223178 0.2182932565375385 chr3 198022430 4762218 0.02404888173526605 0.16647235977069239 chr4 191154276 4570415 0.0239095619289207 0.1763066473571593 chr5 180915260 2579421 0.014257619838149639 0.12911259092568883 chr6 171115067 3795769 0.02218255274972367 0.16627048143180737 chr7 159138663 3092094 0.019430187119267178 0.17373589869394993 chr8 146364022 4589774 0.031358621724674934 0.21109564196506217 chr9 141213431 2576950 0.018248618291839394 0.1946991852014469 chr10 135534747 3396973 0.025063484273888822 0.20336771403129564 chr11 135006516 2282194 0.01690432482532917 0.18422292643117377 chr12 133851895 3192984 0.023854604374484202 0.1667504789450683 chr13 115169878 2229868 0.019361555631759893 0.14829143187673866 chr14 107349540 2534718 0.023611819855026858 0.17347713946675897 chr15 102531392 2084068 0.020326145576956566 0.1527816842452709 chr16 90354753 2113727 0.023393644825745914 0.17341345854270368 chr17 81195210 1620312 0.01995575847392968 0.15566680488037754 chr18 78077248 1756306 0.02249446599347354 0.34578054409181225 chr19 59128983 1338203 0.022631929928509 0.20686647350921214 chr20 63025520 2237413 0.035500111700784064 0.20718776954524604 chr21 48129895 935993 0.019447227133988138 0.16167926735845667 chr22 51304566 854750 0.016660310507255825 0.13769524205871816 chrMT 16571 21100 1.2733087924687707 1.4076659419905575 chrX 155270560 3956186 0.025479305284916858 0.1890019444864033 chrY 59373566 195582 0.0032940921891065123 0.08227822434154067