BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238040.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 = 1,888,765 number of mapped reads = 1,565,766 (82.9%) number of supplementary alignments = 13,641 (0.72%) number of secondary alignments = 0 number of mapped bases = 100,930,569 bp number of sequenced bases = 100,879,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 237,976 duplication rate = 11.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9914 >>>>>>> ACTG content number of A's = 27,899,885 bp (27.66%) number of C's = 18,368,283 bp (18.21%) number of T's = 32,051,137 bp (31.77%) number of G's = 22,373,354 bp (22.18%) number of N's = 186,580 bp (0.18%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 948,277 number of insertions = 8,499 mapped reads with insertion percentage = 0.54% number of deletions = 31,971 mapped reads with deletion percentage = 2.02% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.3877X There is a 1.6% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% 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% 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 8570870 0.034386554246538865 0.5030559001934036 chr2 243199373 7588507 0.03120282304346237 0.4509425495719776 chr3 198022430 7337237 0.0370525551070149 0.34443879933643107 chr4 191154276 5644322 0.029527573843025096 0.3121343569318834 chr5 180915260 6140632 0.03394203451936559 0.32534530626641184 chr6 171115067 6397851 0.037389173917688964 0.368511790889788 chr7 159138663 5650780 0.03550853006726593 0.44924084539480474 chr8 146364022 4706687 0.03215740409210673 0.5257581283798158 chr9 141213431 4418270 0.03128788790635644 0.3719447523256024 chr10 135534747 4096770 0.030226713744483547 0.3385203209140679 chr11 135006516 5111257 0.03785933561903042 0.3979038052796146 chr12 133851895 4030075 0.030108464284349504 0.30927482992095384 chr13 115169878 3331269 0.028924828764687934 0.3064842145081073 chr14 107349540 4008604 0.03734160388577352 0.3543411164033557 chr15 102531392 2602518 0.025382645736439433 0.2814714033127032 chr16 90354753 2758416 0.030528731565455113 0.30727339535626236 chr17 81195210 2441254 0.030066478059481587 0.3101886288129012 chr18 78077248 3332557 0.042682818431305364 0.6184685887396643 chr19 59128983 1661328 0.02809667807071872 0.44320964313988714 chr20 63025520 2771003 0.04396636473606247 0.36984362060209897 chr21 48129895 1182027 0.024559101988483458 0.28341007010610936 chr22 51304566 990090 0.019298282340016286 0.23165029173598833 chrMT 16571 57380 3.4626757588558323 3.7490012332323124 chrX 155270560 5820009 0.03748301674187302 0.35409125909814015 chrY 59373566 280856 0.004730320560499937 0.1307157039379408