BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525197.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 = 979,060 number of mapped reads = 891,958 (91.1%) number of supplementary alignments = 2,081 (0.21%) number of secondary alignments = 0 number of mapped bases = 50,942,146 bp number of sequenced bases = 50,926,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,793 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9942 >>>>>>> ACTG content number of A's = 12,885,620 bp (25.3%) number of C's = 9,522,147 bp (18.7%) number of T's = 16,330,028 bp (32.07%) number of G's = 12,187,612 bp (23.93%) number of N's = 1,164 bp (0%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 264,937 number of insertions = 3,753 mapped reads with insertion percentage = 0.42% number of deletions = 9,941 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.23% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 0.1892X There is a 1.53% 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 4944647 0.019838052880919402 0.29579930478216027 chr2 243199373 3835314 0.015770246249771375 0.23437997513489794 chr3 198022430 4465677 0.02255136955949889 0.1596203748873317 chr4 191154276 2931345 0.015334969540519197 0.1336605639645121 chr5 180915260 2313668 0.012788683497456212 0.11927797940035317 chr6 171115067 3240903 0.018939904339341434 0.15817788805972205 chr7 159138663 3779311 0.02374854060449157 0.33482114356372716 chr8 146364022 2592715 0.017714155190406013 0.1642953319137282 chr9 141213431 1690719 0.011972791738202296 0.13859154683935382 chr10 135534747 2409679 0.017779049677939782 0.20820362223289351 chr11 135006516 2318995 0.017176911668470875 0.16804167552053856 chr12 133851895 2292343 0.017125965979039745 0.13862563557092017 chr13 115169878 1208231 0.010490859424197706 0.10916795731937023 chr14 107349540 2925792 0.027254816369031484 0.17485408375190772 chr15 102531392 981349 0.009571205275356058 0.10679331247382029 chr16 90354753 1223900 0.01354549660492127 0.134192616924743 chr17 81195210 881639 0.010858263683288707 0.112726972271997 chr18 78077248 1094701 0.014020742636830643 0.23366382943435296 chr19 59128983 806899 0.013646421079151658 0.22035522363284604 chr20 63025520 881617 0.013988254281757612 0.12603735136152253 chr21 48129895 637249 0.013240190945772893 0.1230320045174001 chr22 51304566 395028 0.0076996655619306865 0.09181434269854316 chrMT 16571 143465 8.657594592963612 5.6224560284137475 chrX 155270560 2809709 0.018095568148913742 0.15370481140708764 chrY 59373566 137251 0.0023116516195102717 0.06661429559804287