BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472647.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,341,912 number of mapped reads = 8,256,938 (98.98%) number of supplementary alignments = 41,809 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,137,062 number of mapped paired reads (second in pair) = 4,119,876 number of mapped paired reads (both in pair) = 8,203,568 number of mapped paired reads (singletons) = 53,370 number of mapped bases = 811,614,990 bp number of sequenced bases = 811,506,475 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,172,308 duplication rate = 41.82% >>>>>>> Insert size mean insert size = 22,650.9975 std insert size = 1,464,466.0987 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 54.7105 >>>>>>> ACTG content number of A's = 221,312,803 bp (27.27%) number of C's = 185,812,065 bp (22.9%) number of T's = 221,158,439 bp (27.25%) number of G's = 183,119,128 bp (22.57%) number of N's = 104,040 bp (0.01%) GC percentage = 45.46% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 6,732,617 number of insertions = 48,756 mapped reads with insertion percentage = 0.59% number of deletions = 45,165 mapped reads with deletion percentage = 0.54% homopolymer indels = 48.03% >>>>>>> Coverage mean coverageData = 0.2622X std coverageData = 13.9802X There is a 2.14% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 103763142 0.41630043521536503 14.042567870142715 chr2 243199373 60439248 0.24851728544546864 15.108668903704208 chr3 198022430 68422940 0.3455312612818659 13.653350195029637 chr4 191154276 26833465 0.14037595999160385 6.445146817507225 chr5 180915260 47067868 0.2601652729570739 21.518034627332007 chr6 171115067 63479059 0.3709729371756609 14.389140994998156 chr7 159138663 51754874 0.32521873078699925 15.818458796147393 chr8 146364022 49309969 0.33689952165976966 16.046228334424935 chr9 141213431 22088397 0.15641852792316902 4.998265974260136 chr10 135534747 28223811 0.20824040790071346 16.88705079863152 chr11 135006516 24409167 0.18079991783507693 14.119407779859902 chr12 133851895 33260882 0.24849018387076252 9.489633960257306 chr13 115169878 19963140 0.17333646910696562 8.29477312033174 chr14 107349540 29958450 0.279073855370037 11.877255312494464 chr15 102531392 27260047 0.2658702517176398 17.35847424081721 chr16 90354753 42099412 0.4659346697566646 19.570095258577506 chr17 81195210 22702756 0.2796070851962819 18.485306403384758 chr18 78077248 5764935 0.07383629863593553 5.97764875511577 chr19 59128983 11030714 0.18655342000385836 7.669993441604218 chr20 63025520 9075439 0.14399625738907032 5.348919633048417 chr21 48129895 4875669 0.10130229870644845 6.265954014540671 chr22 51304566 10372485 0.20217469532828716 8.658768457071865 chrMT 16571 5295 0.3195341258825659 0.7662194606543462 chrX 155270560 49050927 0.31590616405325 17.49398870191251 chrY 59373566 402899 0.006785831256960378 0.25146040190054875