BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716697.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,146,548 number of mapped reads = 1,062,971 (92.71%) number of supplementary alignments = 17,491 (1.53%) number of secondary alignments = 0 number of mapped bases = 84,330,463 bp number of sequenced bases = 84,293,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,024 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8581 >>>>>>> ACTG content number of A's = 20,441,957 bp (24.25%) number of C's = 17,493,932 bp (20.75%) number of T's = 25,108,798 bp (29.79%) number of G's = 21,244,366 bp (25.2%) number of N's = 4,685 bp (0.01%) GC percentage = 45.96% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 705,010 number of insertions = 7,937 mapped reads with insertion percentage = 0.74% number of deletions = 21,004 mapped reads with deletion percentage = 1.95% homopolymer indels = 44.44% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.3419X There is a 2.42% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8941809 0.03587477120067035 0.5642687874475892 chr2 243199373 8039504 0.033057256278370424 0.6161292127465089 chr3 198022430 5354511 0.027039921689679294 0.18347637807338527 chr4 191154276 3350640 0.017528459577854278 0.15000731317080493 chr5 180915260 4401368 0.02432834024061873 0.17131766180597224 chr6 171115067 6344720 0.037078675251899354 0.254949502748929 chr7 159138663 4543903 0.02855310528780803 0.3369885868828778 chr8 146364022 5689842 0.03887459446830451 0.45644706282084374 chr9 141213431 3020134 0.021387016649995566 0.3205983702880771 chr10 135534747 4684722 0.03456473047461401 0.3837247897314768 chr11 135006516 3305098 0.024481025789895947 0.2669180314915476 chr12 133851895 3249481 0.024276690292655178 0.17196736160907755 chr13 115169878 2349714 0.020402157584989367 0.15470283069078006 chr14 107349540 2239420 0.020861011607502 0.18192312010808107 chr15 102531392 1735007 0.016921715058740253 0.1419065922283628 chr16 90354753 2359314 0.02611167560825494 0.19848145676840415 chr17 81195210 3264573 0.04020647277099228 0.24643303342896755 chr18 78077248 1964197 0.025157098262479742 0.568725098391015 chr19 59128983 1930092 0.03264206319936198 0.44609569264750853 chr20 63025520 1438350 0.02282170777805562 0.18260176342447865 chr21 48129895 1312420 0.027268291360286575 0.1846417874840496 chr22 51304566 1083786 0.021124552539826574 0.16253072880367217 chrMT 16571 38441 2.3197755114356404 2.0207238632873437 chrX 155270560 3495485 0.022512219959791475 0.2033521754668532 chrY 59373566 193932 0.0032663020442464242 0.09515607161759013