BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174048.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,326,366 number of mapped reads = 4,206,404 (97.23%) number of supplementary alignments = 536,441 (12.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,100,809 number of mapped paired reads (second in pair) = 2,105,595 number of mapped paired reads (both in pair) = 4,120,978 number of mapped paired reads (singletons) = 85,426 number of mapped bases = 497,252,655 bp number of sequenced bases = 496,927,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,209,970 duplication rate = 63.58% >>>>>>> Insert size mean insert size = 1,147,930.5669 std insert size = 9,852,037.1267 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.4229 >>>>>>> ACTG content number of A's = 148,062,756 bp (29.8%) number of C's = 98,010,551 bp (19.72%) number of T's = 148,357,978 bp (29.86%) number of G's = 102,490,098 bp (20.62%) number of N's = 6,135 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 5,277,506 number of insertions = 53,190 mapped reads with insertion percentage = 1.22% number of deletions = 142,167 mapped reads with deletion percentage = 3.3% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.1606X std coverageData = 2.4302X There is a 3.78% of reference with a coverageData >= 1X There is a 2.92% of reference with a coverageData >= 2X There is a 2.18% of reference with a coverageData >= 3X There is a 1.72% of reference with a coverageData >= 4X There is a 1.25% of reference with a coverageData >= 5X There is a 0.97% of reference with a coverageData >= 6X There is a 0.68% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 35424991 0.14212598892582098 1.6469424836676514 chr2 243199373 42382654 0.17427123054301624 7.382368497240506 chr3 198022430 40271353 0.20336763365644994 1.224641760370278 chr4 191154276 21948625 0.11482152248584802 1.0580911107794575 chr5 180915260 29991496 0.1657764856320025 1.0838425200096011 chr6 171115067 26640252 0.155686185132955 1.2036857483915278 chr7 159138663 28501342 0.1790975333253868 1.5500714536018896 chr8 146364022 28647388 0.19572697995413108 1.4911019015593314 chr9 141213431 21191986 0.1500706119094295 1.2461518238747797 chr10 135534747 26400643 0.19478874299296844 2.0849333708387183 chr11 135006516 18064546 0.13380499353083075 0.9899890710977038 chr12 133851895 22122196 0.16527368551636867 1.0917460128983627 chr13 115169878 15272249 0.13260627922172497 0.9828563780979017 chr14 107349540 14531709 0.13536815341733183 0.9863147447787398 chr15 102531392 17234478 0.16808976903385844 1.0881895528006362 chr16 90354753 17581613 0.19458426276700685 1.461119202409476 chr17 81195210 21185041 0.26091491111359894 1.4869931090876747 chr18 78077248 9778118 0.12523645812926193 1.6696147086065403 chr19 59128983 8512974 0.14397294808875707 1.3075490412537403 chr20 63025520 21946668 0.34821875329231716 1.7098171199670809 chr21 48129895 6165923 0.12811004470298554 0.998282225668624 chr22 51304566 4024075 0.0784350266212173 0.7154993302963357 chrMT 16571 1197791 72.28236075070907 55.51020361262883 chrX 155270560 17322896 0.11156587572041989 0.8889393946609461 chrY 59373566 911648 0.015354442412975499 0.5822835243601004