BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716511.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 = 2,131,496 number of mapped reads = 1,911,340 (89.67%) number of supplementary alignments = 9,930 (0.47%) number of secondary alignments = 0 number of mapped bases = 110,717,718 bp number of sequenced bases = 110,683,769 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,264 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2054 >>>>>>> ACTG content number of A's = 28,272,612 bp (25.54%) number of C's = 20,409,174 bp (18.44%) number of T's = 34,119,411 bp (30.83%) number of G's = 27,881,213 bp (25.19%) number of N's = 1,359 bp (0%) GC percentage = 43.63% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 559,520 number of insertions = 7,472 mapped reads with insertion percentage = 0.39% number of deletions = 21,443 mapped reads with deletion percentage = 1.11% homopolymer indels = 40.1% >>>>>>> Coverage mean coverageData = 0.0358X std coverageData = 0.3409X There is a 3.15% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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% 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 9129441 0.036627555684204297 0.4634139016228515 chr2 243199373 10784881 0.04434584212517686 0.40879988818272467 chr3 198022430 8356238 0.04219844186337881 0.24470851032377142 chr4 191154276 6106134 0.03194348631782634 0.2164363141944241 chr5 180915260 5550572 0.03068050754811949 0.1950934819401061 chr6 171115067 6096584 0.03562856332224678 0.2278246322458435 chr7 159138663 6848143 0.043032553314840905 0.7785104420886328 chr8 146364022 7805422 0.05332882967646243 0.3662917689308963 chr9 141213431 4589274 0.03249884920648943 0.23406524030973044 chr10 135534747 5200255 0.03836842665888475 0.43876183199733404 chr11 135006516 3297894 0.02442766540246102 0.2183178135466432 chr12 133851895 5164356 0.03858261401528906 0.24256463855648372 chr13 115169878 2872471 0.024941165605819257 0.17486929017173067 chr14 107349540 3535364 0.03293320120421569 0.2052475175093374 chr15 102531392 2642497 0.025772565342719624 0.1852066031804803 chr16 90354753 3340141 0.036966965091476706 0.22568403797141726 chr17 81195210 4629517 0.0570171196059472 0.2767733354420361 chr18 78077248 2590362 0.03317691217805218 0.3789861728141391 chr19 59128983 2216239 0.03748143275185369 0.4092903481197729 chr20 63025520 2469137 0.0391767810880418 0.23200713996168668 chr21 48129895 1426802 0.0296448184646985 0.1994018407267254 chr22 51304566 1686523 0.03287276613937247 0.19965671685662115 chrMT 16571 284686 17.179771890652344 10.278172391036243 chrX 155270560 3849872 0.024794603690487107 0.20184859910891334 chrY 59373566 244913 0.004124950150375 0.11697810753372107