BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082893.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,060,544 number of mapped reads = 3,353,221 (82.58%) number of supplementary alignments = 22,916 (0.56%) number of secondary alignments = 0 number of mapped bases = 227,209,549 bp number of sequenced bases = 227,126,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 162,705 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3818 >>>>>>> ACTG content number of A's = 64,312,374 bp (28.32%) number of C's = 41,359,356 bp (18.21%) number of T's = 73,317,070 bp (32.28%) number of G's = 48,125,794 bp (21.19%) number of N's = 12,016 bp (0.01%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 2,026,436 number of insertions = 18,970 mapped reads with insertion percentage = 0.56% number of deletions = 48,619 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.0734X std coverageData = 0.6014X There is a 5.86% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% 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 23737718 0.0952363444663193 1.2634965703032561 chr2 243199373 22533021 0.0926524633762111 0.6479274602032731 chr3 198022430 16643482 0.0840484686507483 0.3461673337020544 chr4 191154276 13152568 0.06880603602087353 0.329064268160979 chr5 180915260 13235139 0.07315656512336217 0.3251388122665072 chr6 171115067 16270934 0.09508767571005305 0.5802483011829612 chr7 159138663 11701848 0.07353240111109895 0.5662673972059888 chr8 146364022 18056298 0.12336568613835988 0.8787329595672693 chr9 141213431 6576825 0.046573650632424614 0.5109037534134726 chr10 135534747 8511304 0.06279794804206186 0.4734950960234278 chr11 135006516 9305012 0.06892268814640028 0.4429025780491235 chr12 133851895 7400049 0.055285351021739364 0.2926432988991891 chr13 115169878 5542807 0.04812722819763689 0.2588800442629332 chr14 107349540 5050108 0.047043592361923486 0.3022053901790461 chr15 102531392 4297346 0.041912490566791485 0.2420908594141564 chr16 90354753 7233065 0.08005184851758712 0.4020912056016459 chr17 81195210 5515799 0.06793256646543558 0.4109522735059792 chr18 78077248 6216562 0.07962065978554982 1.127900887125029 chr19 59128983 3853985 0.06517928779529321 0.7736622230810729 chr20 63025520 4449439 0.07059741831562834 0.3388018048636608 chr21 48129895 5351509 0.11118887751573113 0.4166786328414242 chr22 51304566 2739443 0.05339569581389696 0.27173300553074653 chrMT 16571 147984 8.930299921549695 5.965547344074375 chrX 155270560 9294699 0.059861309188296866 0.3482357835541895 chrY 59373566 392605 0.006612454438057502 0.13809193584994123