BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525255.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 = 1,656,870 number of mapped reads = 1,518,240 (91.63%) number of supplementary alignments = 6,023 (0.36%) number of secondary alignments = 0 number of mapped bases = 88,001,500 bp number of sequenced bases = 87,971,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,010 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0975 >>>>>>> ACTG content number of A's = 22,663,333 bp (25.76%) number of C's = 15,197,434 bp (17.28%) number of T's = 28,170,452 bp (32.02%) number of G's = 21,938,574 bp (24.94%) number of N's = 1,839 bp (0%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 442,187 number of insertions = 6,022 mapped reads with insertion percentage = 0.39% number of deletions = 18,593 mapped reads with deletion percentage = 1.21% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 0.0284X std coverageData = 0.2797X There is a 2.58% of reference with a coverageData >= 1X There is a 0.19% 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 9922938 0.03981108636836656 0.4899044067561007 chr2 243199373 7221575 0.029694052706295423 0.36362516158339364 chr3 198022430 7280321 0.03676513312153578 0.2088093916619858 chr4 191154276 4949354 0.025891934533549227 0.1812806671638033 chr5 180915260 3795079 0.020977108288156566 0.1569869950888523 chr6 171115067 5473309 0.03198613129725157 0.21388798855006938 chr7 159138663 6356502 0.03994316579120688 0.49456937227902686 chr8 146364022 4938690 0.03374251358028409 0.2918135205900111 chr9 141213431 2847517 0.020164632923620418 0.20000388625735704 chr10 135534747 4581543 0.033803457057399455 0.28818229525580846 chr11 135006516 3886858 0.028790151136112573 0.21926022485818064 chr12 133851895 3853374 0.028788341024234287 0.18723473826386988 chr13 115169878 2686154 0.02332340753195901 0.16555225448158806 chr14 107349540 3173556 0.02956282812203946 0.1903149391129892 chr15 102531392 2334685 0.02277044088116935 0.16637834698965193 chr16 90354753 2298341 0.025436857759989672 0.18642916094458947 chr17 81195210 1949247 0.024006921097931764 0.17160282669403162 chr18 78077248 1844344 0.023622041596548075 0.36480247404041044 chr19 59128983 1457047 0.024641841040966322 0.3569603899973357 chr20 63025520 1558357 0.02472580948161951 0.17135574418145696 chr21 48129895 1097614 0.02280524401725788 0.16832391189078105 chr22 51304566 722063 0.014074049471542163 0.12698934293462888 chrMT 16571 22867 1.3799408605394967 1.2847764968462685 chrX 155270560 3518022 0.022657366599308976 0.1793062214179854 chrY 59373566 232143 0.003909871271669955 0.12033713442934393