BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708643.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,646,216 number of mapped reads = 4,447,875 (95.73%) number of supplementary alignments = 114 (0%) number of secondary alignments = 0 number of mapped bases = 221,843,435 bp number of sequenced bases = 221,821,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,613 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5253 >>>>>>> ACTG content number of A's = 68,502,468 bp (30.88%) number of C's = 42,269,042 bp (19.06%) number of T's = 68,423,908 bp (30.85%) number of G's = 42,617,797 bp (19.21%) number of N's = 7,785 bp (0%) GC percentage = 38.27% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 364,493 number of insertions = 15,294 mapped reads with insertion percentage = 0.34% number of deletions = 13,022 mapped reads with deletion percentage = 0.29% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.0717X std coverageData = 0.2791X There is a 6.65% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.04% 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 17748084 0.07120577645421393 0.27989389768460055 chr2 243199373 18540821 0.07623712500278526 0.28692905181307177 chr3 198022430 18481687 0.09333128070390814 0.31712323636271167 chr4 191154276 16912847 0.08847747146393942 0.3083050363913855 chr5 180915260 16584050 0.09166750223281331 0.31375998074853534 chr6 171115067 13775449 0.08050400962061395 0.2944119206565403 chr7 159138663 12033127 0.07561410139533471 0.2865817025574124 chr8 146364022 11050347 0.07549906629376446 0.28490182583387874 chr9 141213431 9415764 0.06667753862591158 0.269392714908952 chr10 135534747 9223048 0.06804932465030536 0.2699749534774215 chr11 135006516 10904605 0.08077095330717222 0.2976523184933205 chr12 133851895 10337453 0.077230531551309 0.2894751093699041 chr13 115169878 8304245 0.07210431359491412 0.28022124531022996 chr14 107349540 7426327 0.06917893639786439 0.27485864772950896 chr15 102531392 5566679 0.05429243562790994 0.24317600427607292 chr16 90354753 4490131 0.04969446377657631 0.23112503310249857 chr17 81195210 3705804 0.045640672645590796 0.22309743695562415 chr18 78077248 9324068 0.11942106361125843 0.3606251431336893 chr19 59128983 1960071 0.03314907344169948 0.18772931123810008 chr20 63025520 3526493 0.05595341379174658 0.2446341057687153 chr21 48129895 2180519 0.04530487756102522 0.22273866956693883 chr22 51304566 1367411 0.026652812928970104 0.16950124649565368 chrMT 16571 500 0.03017319413433106 0.1710636504055231 chrX 155270560 8128499 0.0523505486165568 0.2365921003250626 chrY 59373566 855406 0.014407185851023333 0.124637744914054