BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231825.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 = 1,680,554 number of mapped reads = 668,059 (39.75%) number of supplementary alignments = 8,625 (0.51%) number of secondary alignments = 0 number of mapped bases = 42,479,987 bp number of sequenced bases = 42,459,395 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,570 duplication rate = 9.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8245 >>>>>>> ACTG content number of A's = 11,524,757 bp (27.14%) number of C's = 8,154,999 bp (19.21%) number of T's = 13,180,737 bp (31.04%) number of G's = 9,594,111 bp (22.6%) number of N's = 4,791 bp (0.01%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 356,861 number of insertions = 4,135 mapped reads with insertion percentage = 0.61% number of deletions = 11,867 mapped reads with deletion percentage = 1.75% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 0.2061X There is a 0.8% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.06% 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% 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 3260100 0.013079606329245616 0.2771481005898057 chr2 243199373 3261570 0.013411095430743565 0.2177651274791965 chr3 198022430 2743967 0.013856849448822539 0.18582819125528852 chr4 191154276 2623502 0.013724526884242966 0.18912731517462353 chr5 180915260 3149052 0.01740622653943067 0.2121753788434143 chr6 171115067 2386635 0.013947544432191936 0.19296807600857974 chr7 159138663 2528193 0.015886730178196858 0.22525415583267547 chr8 146364022 1945083 0.013289351941968362 0.19975972733652841 chr9 141213431 1296182 0.009178886107511969 0.15788177283113947 chr10 135534747 2528595 0.01865643354172491 0.2328493361771897 chr11 135006516 2142403 0.015868885913625088 0.2073925589650347 chr12 133851895 2140104 0.01598859694888892 0.20142473306757386 chr13 115169878 1179999 0.01024572588329042 0.19278312199172712 chr14 107349540 1297578 0.012087410900875775 0.18567942209362753 chr15 102531392 1229971 0.011996043124041464 0.17420279657180252 chr16 90354753 1117650 0.012369576174924632 0.18543364795556402 chr17 81195210 1015878 0.012511550866116362 0.18311047293946459 chr18 78077248 1065153 0.01364229692112099 0.22666465103117037 chr19 59128983 883840 0.014947661115700232 0.23604428576624303 chr20 63025520 886059 0.014058733668520307 0.1924620095619154 chr21 48129895 600398 0.01247453375911167 0.17702682253726815 chr22 51304566 394255 0.007684598676850712 0.13758068680786226 chrMT 16571 48327 2.9163599058596343 3.063897524554026 chrX 155270560 2591243 0.016688566074599075 0.20932221166096876 chrY 59373566 164250 0.0027663826019814946 0.08815779814579998