BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008659.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 = 2,211,833 number of mapped reads = 1,989,907 (89.97%) number of supplementary alignments = 12,098 (0.55%) number of secondary alignments = 0 number of mapped bases = 126,518,300 bp number of sequenced bases = 126,455,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,635 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1277 >>>>>>> ACTG content number of A's = 32,815,730 bp (25.95%) number of C's = 23,363,617 bp (18.48%) number of T's = 39,629,970 bp (31.34%) number of G's = 30,587,408 bp (24.19%) number of N's = 58,531 bp (0.05%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 964,942 number of insertions = 8,503 mapped reads with insertion percentage = 0.42% number of deletions = 36,409 mapped reads with deletion percentage = 1.81% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0409X std coverageData = 0.2862X There is a 3.39% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12555117 0.05037145724904733 0.40821613199134926 chr2 243199373 12811882 0.052680571672362 0.33248948259312566 chr3 198022430 9655577 0.04876001673143795 0.25859201892713746 chr4 191154276 5871666 0.030716895917096827 0.21468347908805846 chr5 180915260 4878350 0.026964834254445978 0.19120234402616693 chr6 171115067 6543936 0.03824289768708678 0.2492043300021327 chr7 159138663 5940889 0.037331525149234164 0.32702217012848844 chr8 146364022 9453486 0.06458886460499152 0.3257217040832015 chr9 141213431 4564352 0.03232236457734675 0.27458768894363994 chr10 135534747 8092140 0.05970527985712771 0.3329299955132629 chr11 135006516 5952867 0.04409318288015076 0.30780372818488927 chr12 133851895 6071062 0.045356563685557086 0.25099031328146926 chr13 115169878 2013897 0.0174863170385576 0.1512731154321595 chr14 107349540 4286854 0.03993360381423153 0.239300825275093 chr15 102531392 3848161 0.03753153960886438 0.24004542755673952 chr16 90354753 3348370 0.03705803943706204 0.2646220176579034 chr17 81195210 3696069 0.04552077641033258 0.2715056473031046 chr18 78077248 1441109 0.01845747688238192 0.40007586944052 chr19 59128983 3438851 0.0581584668892411 0.3549522978703397 chr20 63025520 2919005 0.04631465158875325 0.25624218161243145 chr21 48129895 1509626 0.03136566161218511 0.21925819255633863 chr22 51304566 2101320 0.040957758028788316 0.23715156322088723 chrMT 16571 37723 2.2764468046587414 2.2666401837887205 chrX 155270560 5190303 0.033427476528712204 0.2273813170568378 chrY 59373566 295688 0.004980128699024074 0.1516089688413402