BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716876.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 = 831,982 number of mapped reads = 757,996 (91.11%) number of supplementary alignments = 1,401 (0.17%) number of secondary alignments = 0 number of mapped bases = 43,438,419 bp number of sequenced bases = 43,425,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,911 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5717 >>>>>>> ACTG content number of A's = 10,565,246 bp (24.33%) number of C's = 8,297,784 bp (19.11%) number of T's = 13,889,625 bp (31.99%) number of G's = 10,672,244 bp (24.58%) number of N's = 435 bp (0%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 210,024 number of insertions = 2,754 mapped reads with insertion percentage = 0.36% number of deletions = 8,505 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.014X std coverageData = 0.1545X There is a 1.31% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5034913 0.020200202429987126 0.21346101580655522 chr2 243199373 4430856 0.018219027234087484 0.2051777538758844 chr3 198022430 2753039 0.013902662440815417 0.125776059628924 chr4 191154276 1868936 0.00977710799417325 0.10672935722466097 chr5 180915260 3099445 0.017132026342056496 0.13747894132292027 chr6 171115067 1528309 0.00893146948889077 0.10792872866451642 chr7 159138663 2953727 0.01856071267860281 0.23878097452587335 chr8 146364022 1930738 0.013191342883430738 0.13302337574520132 chr9 141213431 1174513 0.008317289592659214 0.12120178506775016 chr10 135534747 1981320 0.014618539111597707 0.18152768811568645 chr11 135006516 1832451 0.013573055984942238 0.1491107230579931 chr12 133851895 1766704 0.013198946492315256 0.12148028413478533 chr13 115169878 1286534 0.01117075074091856 0.11172110919270582 chr14 107349540 926446 0.008630181368266692 0.10026258706992545 chr15 102531392 1832862 0.017876105690635705 0.14107365231081356 chr16 90354753 1307402 0.014469653854291428 0.1396277105578754 chr17 81195210 1544587 0.019023129566386982 0.15052189239162594 chr18 78077248 1375933 0.017622713853848948 0.21792589994163666 chr19 59128983 650402 0.010999715655518716 0.15531037310392207 chr20 63025520 1088272 0.017267164158264778 0.1384429680242466 chr21 48129895 536605 0.011149099743516997 0.11242096524869846 chr22 51304566 475865 0.009275295302176419 0.10065155008339595 chrMT 16571 21414 1.2922575583851306 1.3667584676582991 chrX 155270560 1931566 0.012440001504470648 0.12778290811391943 chrY 59373566 105580 0.0017782324208049083 0.051899232842292885