BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524358.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 = 3,773,716 number of mapped reads = 3,448,453 (91.38%) number of supplementary alignments = 14,231 (0.38%) number of secondary alignments = 0 number of mapped bases = 199,498,593 bp number of sequenced bases = 199,443,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 266,500 duplication rate = 5.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4951 >>>>>>> ACTG content number of A's = 50,051,216 bp (25.1%) number of C's = 37,349,548 bp (18.73%) number of T's = 64,241,897 bp (32.21%) number of G's = 47,772,412 bp (23.95%) number of N's = 28,168 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,036,523 number of insertions = 14,926 mapped reads with insertion percentage = 0.43% number of deletions = 34,955 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.1% >>>>>>> Coverage mean coverageData = 0.0644X std coverageData = 0.5947X There is a 5.2% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 15411793 0.06183251595589806 1.219802201669276 chr2 243199373 16987609 0.06985054603738637 0.8936679795621199 chr3 198022430 13231602 0.06681870331557895 0.3217438080562051 chr4 191154276 12877451 0.06736679539410356 0.39251293225585 chr5 180915260 11997292 0.06631442809191442 0.31621530094884626 chr6 171115067 11631272 0.06797339476832862 0.3612546275480973 chr7 159138663 11070172 0.06956305772155444 0.7276280931455541 chr8 146364022 10401801 0.07106801834128335 0.4687968922061183 chr9 141213431 8505632 0.06023245763358019 0.46496563762962345 chr10 135534747 8059606 0.05946523809130658 0.5415960377106182 chr11 135006516 9355995 0.06930032177113585 0.48171815655359773 chr12 133851895 8788316 0.06565701591299847 0.32574857214324776 chr13 115169878 5993957 0.05204448510399568 0.27698618959254945 chr14 107349540 6274870 0.05845269574513314 0.3263376847635629 chr15 102531392 5929916 0.057835126241141836 0.2964608364698111 chr16 90354753 6175834 0.06835095880346218 0.3656409553839975 chr17 81195210 5691323 0.0700943196033362 0.36221094108719837 chr18 78077248 5174355 0.0662722512965621 0.9590476873884961 chr19 59128983 4431824 0.07495180493802844 0.783579724136645 chr20 63025520 4435680 0.07037910992245681 0.33837469829404443 chr21 48129895 2551314 0.053008925118162006 0.3485645631075998 chr22 51304566 2540379 0.04951565129700152 0.2746961599982116 chrMT 16571 43530 2.626878281334862 2.467250138303939 chrX 155270560 11276731 0.07262633045182551 0.3999233152768598 chrY 59373566 660339 0.011121767555615576 0.2875639605798128