BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524349.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 = 2,890,495 number of mapped reads = 2,658,426 (91.97%) number of supplementary alignments = 11,446 (0.4%) number of secondary alignments = 0 number of mapped bases = 154,955,211 bp number of sequenced bases = 154,913,335 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,020 duplication rate = 4.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8092 >>>>>>> ACTG content number of A's = 38,667,138 bp (24.96%) number of C's = 32,304,598 bp (20.85%) number of T's = 46,508,240 bp (30.02%) number of G's = 37,412,292 bp (24.15%) number of N's = 21,067 bp (0.01%) GC percentage = 45% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 789,592 number of insertions = 11,639 mapped reads with insertion percentage = 0.43% number of deletions = 25,871 mapped reads with deletion percentage = 0.97% homopolymer indels = 41.24% >>>>>>> Coverage mean coverageData = 0.0501X std coverageData = 0.4544X There is a 4.15% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 12557572 0.05038130677315344 0.8617936512876967 chr2 243199373 12839968 0.052796057167466465 0.6399563740039436 chr3 198022430 9824490 0.04961301606085735 0.26421336215540625 chr4 191154276 9623044 0.050341766877346754 0.32424371614067937 chr5 180915260 9146066 0.05055441978747398 0.26636826183281226 chr6 171115067 8549137 0.049961333913395245 0.2915251261566381 chr7 159138663 8567967 0.05383963166763566 0.5882086743007745 chr8 146364022 7907699 0.0540276147918373 0.37004364647458127 chr9 141213431 6421377 0.04547284882554833 0.3616595990440644 chr10 135534747 7665903 0.05656042579250913 0.4438423884989467 chr11 135006516 7035594 0.05211299579051429 0.3989316187546027 chr12 133851895 6964404 0.05203067166139112 0.27456887890415776 chr13 115169878 4651427 0.04038753084378539 0.23521571982131698 chr14 107349540 4715780 0.043929205472142685 0.2654129081979494 chr15 102531392 4517073 0.04405551228642248 0.2504007109791022 chr16 90354753 4790491 0.05301869399167081 0.30047211482503877 chr17 81195210 4629651 0.05701876994960663 0.3058331251984341 chr18 78077248 4056315 0.05195258675100844 0.7527725591996831 chr19 59128983 3526557 0.0596417665428137 0.576877055901899 chr20 63025520 3445451 0.0546675537147492 0.2890742798390753 chr21 48129895 2039210 0.042368885284291606 0.2951263825344044 chr22 51304566 2082397 0.04058892146168822 0.24055850533234654 chrMT 16571 335076 20.22062639551023 11.723097536790412 chrX 155270560 8536862 0.054980557808254185 0.3240590528226128 chrY 59373566 525700 0.008854108577544425 0.23921332004584248