BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231890.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,487,153 number of mapped reads = 3,248,353 (93.15%) number of supplementary alignments = 35,189 (1.01%) number of secondary alignments = 0 number of mapped bases = 223,098,667 bp number of sequenced bases = 223,017,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 532,503 duplication rate = 6.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3831 >>>>>>> ACTG content number of A's = 56,130,818 bp (25.17%) number of C's = 40,002,430 bp (17.94%) number of T's = 61,301,904 bp (27.49%) number of G's = 65,536,128 bp (29.39%) number of N's = 45,875 bp (0.02%) GC percentage = 47.32% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,486,376 number of insertions = 15,279 mapped reads with insertion percentage = 0.47% number of deletions = 49,540 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.0721X std coverageData = 40.3942X There is a 3.72% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 16648906 0.0667958456159674 0.661600767722567 chr2 243199373 43863777 0.1803613901586827 144.10239133151705 chr3 198022430 6751690 0.03409558200048348 0.2855739382002403 chr4 191154276 3448794 0.018041940113335472 0.23584359740133362 chr5 180915260 5983714 0.033074678167004816 0.2929614219237052 chr6 171115067 27264507 0.1593343442982727 0.9428955482321347 chr7 159138663 4785451 0.030070951394131042 0.3884516852209412 chr8 146364022 9477555 0.0647533107555626 0.6381895862440192 chr9 141213431 22286262 0.15781970484096516 0.9098953768754808 chr10 135534747 1755251 0.01295056093622988 0.2829384387488644 chr11 135006516 12310685 0.09118585802184541 1.0067696510247237 chr12 133851895 1501593 0.01121831708097969 0.25194786828571514 chr13 115169878 1556905 0.013518335063270624 0.17594231863780024 chr14 107349540 4570888 0.04257948380589242 0.5339180815200991 chr15 102531392 4588679 0.044753893519752466 0.35645474536881194 chr16 90354753 12332704 0.13649203379483535 0.6518297088562846 chr17 81195210 5998676 0.07387967837018958 0.5495596801120078 chr18 78077248 6955881 0.08908973072411569 1.3805131303339657 chr19 59128983 8456006 0.1430094950220943 0.8836879461605608 chr20 63025520 3846961 0.061038147721748266 0.42312543529693686 chr21 48129895 11982785 0.24896761150216512 0.8876410731128367 chr22 51304566 4610686 0.08986892121843502 0.4755985126135037 chrMT 16571 9466 0.5712389113511557 1.1270512616035286 chrX 155270560 1684114 0.01084631883854866 0.3035585471518905 chrY 59373566 426731 0.007187222003812269 0.20190884509599671