BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818886.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,383,355 number of mapped reads = 1,364,036 (98.6%) number of supplementary alignments = 20,586 (1.49%) number of secondary alignments = 0 number of mapped bases = 126,245,232 bp number of sequenced bases = 126,165,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,842 duplication rate = 13.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2502 >>>>>>> ACTG content number of A's = 36,657,721 bp (29.06%) number of C's = 27,216,470 bp (21.57%) number of T's = 35,704,048 bp (28.3%) number of G's = 26,585,573 bp (21.07%) number of N's = 1,798 bp (0%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 765,727 number of insertions = 17,519 mapped reads with insertion percentage = 1.24% number of deletions = 40,871 mapped reads with deletion percentage = 2.93% homopolymer indels = 41.75% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.5235X There is a 3.13% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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% 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 11917275 0.047812418489420735 0.8333224582932653 chr2 243199373 9507060 0.03909163038837275 0.6976027096640128 chr3 198022430 7723839 0.039004869296877125 0.24297070359260395 chr4 191154276 6341651 0.03317556443257382 0.29438891954468577 chr5 180915260 5593310 0.03091673969348965 0.23082319327360273 chr6 171115067 6267383 0.03662671622014443 0.26533244961892866 chr7 159138663 11256974 0.07073688937552529 1.1791262252328027 chr8 146364022 11011615 0.07523443841957281 0.42628034345615506 chr9 141213431 4637672 0.032841578645589314 0.43192674895437577 chr10 135534747 5899477 0.04352741367495968 0.6861341997358987 chr11 135006516 5563476 0.0412089443149544 0.31871233261401344 chr12 133851895 4890593 0.03653734599723075 0.2393779240369271 chr13 115169878 3917157 0.03401199226763095 0.2245366630907379 chr14 107349540 3763038 0.03505406730201173 0.25046244649299154 chr15 102531392 3484376 0.03398350429105654 0.22445389395471593 chr16 90354753 3146678 0.034825815970079624 0.5167932160376605 chr17 81195210 3128005 0.03852450163008384 0.31959084060977827 chr18 78077248 2454243 0.0314335233741845 0.4981212701997211 chr19 59128983 2212066 0.03741085822497573 0.6936386767024253 chr20 63025520 5194608 0.08242070830990367 0.380084958649778 chr21 48129895 1201930 0.024972628758072296 0.22761757343511457 chr22 51304566 1460260 0.028462573876952783 0.23515240716856017 chrMT 16571 21340 1.2877919256532497 1.5318624160614178 chrX 155270560 5173302 0.03331798378263078 0.2887174693817004 chrY 59373566 477904 0.008049103872251837 0.6048157462986279