BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004143.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 = 4,991,597 number of mapped reads = 4,035,571 (80.85%) number of supplementary alignments = 26,071 (0.52%) number of secondary alignments = 0 number of mapped bases = 271,234,178 bp number of sequenced bases = 271,102,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 228,479 duplication rate = 4.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8828 >>>>>>> ACTG content number of A's = 75,384,608 bp (27.81%) number of C's = 49,019,774 bp (18.08%) number of T's = 87,006,844 bp (32.09%) number of G's = 59,661,907 bp (22.01%) number of N's = 29,424 bp (0.01%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 2,634,377 number of insertions = 24,913 mapped reads with insertion percentage = 0.61% number of deletions = 77,745 mapped reads with deletion percentage = 1.9% homopolymer indels = 47.02% >>>>>>> Coverage mean coverageData = 0.0876X std coverageData = 0.8445X There is a 6.89% of reference with a coverageData >= 1X There is a 1.26% 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 0.03% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 22298066 0.08946042304945752 1.8035931569165138 chr2 243199373 24741614 0.10173387248000841 0.9568730692856916 chr3 198022430 13144976 0.06638124782126954 0.32301805607236955 chr4 191154276 21117282 0.11047245419715329 0.43295364286865007 chr5 180915260 13077924 0.07228756711843987 0.3413998697625682 chr6 171115067 17893343 0.10456906755031689 0.5319544355344872 chr7 159138663 16316639 0.10253095440421037 1.093821765252151 chr8 146364022 18226722 0.12453007064809957 1.2349273841036619 chr9 141213431 8832102 0.06254434820721834 0.7192298008504554 chr10 135534747 13327951 0.0983360451471533 0.7946182083241422 chr11 135006516 13698303 0.10146401378137926 0.6374369330299652 chr12 133851895 14229180 0.10630540568738306 0.40728716939927423 chr13 115169878 5111346 0.044380927450491874 0.25336658368563186 chr14 107349540 6175180 0.057524047145427915 0.3729670835031092 chr15 102531392 7334006 0.07152937121930424 0.32732043578811737 chr16 90354753 7406103 0.08196694422926484 0.4635201889300644 chr17 81195210 7303723 0.08995263390537447 0.42854819377852615 chr18 78077248 8313926 0.106483338142246 1.500042573148024 chr19 59128983 5037917 0.0852021588127095 1.2233561694020674 chr20 63025520 6856294 0.10878599652965973 0.43723547740577856 chr21 48129895 3922632 0.08150094655307268 0.4028646234887204 chr22 51304566 2110612 0.041138872512828585 0.23826436238177073 chrMT 16571 139261 8.403898376682156 5.6015293896649085 chrX 155270560 13981064 0.09004323807423635 0.4935536532509133 chrY 59373566 638012 0.010745724789378491 0.23833731691397844