BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525264.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 = 1,649,686 number of mapped reads = 1,520,216 (92.15%) number of supplementary alignments = 6,502 (0.39%) number of secondary alignments = 0 number of mapped bases = 88,512,734 bp number of sequenced bases = 88,483,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,340 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1915 >>>>>>> ACTG content number of A's = 22,849,442 bp (25.82%) number of C's = 17,644,655 bp (19.94%) number of T's = 27,433,086 bp (31%) number of G's = 20,554,404 bp (23.23%) number of N's = 1,745 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 435,780 number of insertions = 5,471 mapped reads with insertion percentage = 0.36% number of deletions = 18,681 mapped reads with deletion percentage = 1.22% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0286X std coverageData = 0.2792X There is a 2.58% of reference with a coverageData >= 1X There is a 0.2% 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 9521892 0.03820207934406711 0.5132997177474127 chr2 243199373 7508797 0.030875067264256473 0.3663479448467205 chr3 198022430 7006420 0.03538195142843162 0.20519969273923122 chr4 191154276 5129378 0.026833707868507216 0.1863115229133987 chr5 180915260 4082546 0.022566067671682313 0.16300803279141535 chr6 171115067 4685535 0.027382363705003254 0.2045793629889279 chr7 159138663 5703579 0.035840309906336215 0.4100188170522082 chr8 146364022 4311275 0.029455838539337215 0.2672300792837513 chr9 141213431 2885407 0.02043295017738079 0.20311721398050162 chr10 135534747 4805421 0.035455269636501405 0.2976774663904319 chr11 135006516 4191352 0.031045553386475064 0.23289145753478527 chr12 133851895 4029865 0.03010689538612808 0.19255756156130338 chr13 115169878 2830262 0.024574672207258914 0.17165201295209692 chr14 107349540 3339287 0.03110667265085626 0.19603941193257446 chr15 102531392 2441262 0.023809898143195014 0.17017817548037445 chr16 90354753 2353418 0.026046421708440726 0.19513144657678372 chr17 81195210 1744317 0.02148300373876735 0.16445498495748212 chr18 78077248 1921905 0.02461542958071473 0.38477149259675003 chr19 59128983 1557722 0.026344474756144546 0.34786830445481554 chr20 63025520 1618432 0.025678994794489596 0.17571525679217948 chr21 48129895 1147323 0.023838053251518623 0.17434263248599788 chr22 51304566 709777 0.013834577608550475 0.12656363839963738 chrMT 16571 172304 10.397924084243558 6.102499924779775 chrX 155270560 4553771 0.029327974343623157 0.2007899684550908 chrY 59373566 261487 0.004404097944866576 0.12030547001846031