BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080813.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 = 2,866,227 number of mapped reads = 2,700,673 (94.22%) number of supplementary alignments = 19,786 (0.69%) number of secondary alignments = 0 number of mapped bases = 192,491,582 bp number of sequenced bases = 192,414,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,786 duplication rate = 3.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0166 >>>>>>> ACTG content number of A's = 57,306,388 bp (29.78%) number of C's = 36,511,480 bp (18.98%) number of T's = 60,299,559 bp (31.34%) number of G's = 38,269,573 bp (19.89%) number of N's = 27,322 bp (0.01%) GC percentage = 38.86% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,598,766 number of insertions = 15,383 mapped reads with insertion percentage = 0.56% number of deletions = 42,974 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0622X std coverageData = 0.5747X There is a 4.63% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.07% 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% 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 16289597 0.06535428852552387 1.1008382924700504 chr2 243199373 16865378 0.06934795016926298 0.538573989858942 chr3 198022430 11989255 0.0605449342279054 0.31484316003415774 chr4 191154276 15142637 0.07921683635264325 0.3897580419329447 chr5 180915260 12521346 0.0692111102181209 0.33516940396379147 chr6 171115067 11760475 0.06872845977964057 0.41411388712677455 chr7 159138663 9485254 0.05960370548042118 0.6689066524370638 chr8 146364022 9275826 0.06337504171619443 1.0617495986609025 chr9 141213431 8039902 0.0569344002412915 0.4666505486340769 chr10 135534747 9032857 0.06664606088060945 0.6176607352091766 chr11 135006516 8412018 0.06230823703353696 0.40717186983119874 chr12 133851895 7792739 0.05821911598636687 0.31276379133705695 chr13 115169878 5945691 0.051625399828937914 0.2869638988787699 chr14 107349540 5974818 0.05565760225893842 0.32107115220296367 chr15 102531392 6245842 0.06091638744161398 0.30853252132090064 chr16 90354753 5306770 0.058732604802760074 0.38984296960983006 chr17 81195210 5036082 0.06202437311265036 0.3367030027525172 chr18 78077248 5080270 0.06506722675471349 0.9533652299539354 chr19 59128983 3032412 0.051284697387742995 0.7620215355442923 chr20 63025520 4096339 0.06499492586495122 0.33323613131552265 chr21 48129895 2611953 0.05426882813685756 0.32800424784063315 chr22 51304566 1999502 0.03897317833270435 0.24502887255136505 chrMT 16571 55938 3.3756562669724217 2.760700204789582 chrX 155270560 9985277 0.06430888766035235 0.34738528514204603 chrY 59373566 513404 0.008647013049544641 0.26905662706207284