BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237337.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 = 2,601,237 number of mapped reads = 2,253,431 (86.63%) number of supplementary alignments = 28,317 (1.09%) number of secondary alignments = 0 number of mapped bases = 134,714,093 bp number of sequenced bases = 134,624,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 893,374 duplication rate = 23.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9864 >>>>>>> ACTG content number of A's = 35,125,704 bp (26.09%) number of C's = 23,012,974 bp (17.09%) number of T's = 45,590,309 bp (33.86%) number of G's = 30,881,777 bp (22.94%) number of N's = 13,257 bp (0.01%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 917,359 number of insertions = 8,795 mapped reads with insertion percentage = 0.39% number of deletions = 52,742 mapped reads with deletion percentage = 2.31% homopolymer indels = 40.24% >>>>>>> Coverage mean coverageData = 0.0435X std coverageData = 1.0234X There is a 1.26% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 13461294 0.0540070630355621 0.9091657055092626 chr2 243199373 12412178 0.05103704769830965 1.5330337876076718 chr3 198022430 6684729 0.03375743343822212 0.48856554929144713 chr4 191154276 14759843 0.07721429679135193 0.7704226909129015 chr5 180915260 3807456 0.02104552153311998 0.3687334600585768 chr6 171115067 5182683 0.030287706926474218 0.7897381695266192 chr7 159138663 8927499 0.056098868946762484 0.8883957204189417 chr8 146364022 8817031 0.060240425751623576 1.2457014535840327 chr9 141213431 2583355 0.018293975167277113 0.3811962763097789 chr10 135534747 9658503 0.07126219079451264 0.7954898454255441 chr11 135006516 5704395 0.04225273837893869 0.5526013481720584 chr12 133851895 3467044 0.02590209126288425 0.41386169994413496 chr13 115169878 3059880 0.026568405325566116 0.6878134479474045 chr14 107349540 1392881 0.01297519300036125 0.29415014005822177 chr15 102531392 2354415 0.022962869752124304 0.427443839953752 chr16 90354753 3279255 0.03629311011452823 0.5395120999365767 chr17 81195210 2120690 0.026118412650204367 0.4115897587619517 chr18 78077248 7679030 0.09835169907627891 4.169909058046239 chr19 59128983 1305169 0.022073252976463335 0.5937663791186986 chr20 63025520 1658527 0.026315165666225365 0.41398425679917233 chr21 48129895 1365831 0.028378017446329354 0.4500046190946245 chr22 51304566 673254 0.013122691652824819 0.270785422384274 chrMT 16571 16469 0.9938446683965965 3.1857420084180936 chrX 155270560 13671640 0.08805043274140313 0.8096023172865024 chrY 59373566 671042 0.011302032961941346 0.5868478835978801