BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717010.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 = 1,009,264 number of mapped reads = 937,982 (92.94%) number of supplementary alignments = 14,683 (1.45%) number of secondary alignments = 0 number of mapped bases = 74,829,088 bp number of sequenced bases = 74,795,346 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,491 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8654 >>>>>>> ACTG content number of A's = 18,551,102 bp (24.8%) number of C's = 14,611,186 bp (19.53%) number of T's = 23,173,768 bp (30.98%) number of G's = 18,454,378 bp (24.67%) number of N's = 4,912 bp (0.01%) GC percentage = 44.21% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 604,223 number of insertions = 7,251 mapped reads with insertion percentage = 0.76% number of deletions = 18,953 mapped reads with deletion percentage = 1.99% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.3422X There is a 2.17% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 6292027 0.02524377662433186 0.5662602412308008 chr2 243199373 6620428 0.02722222478756144 0.5609857969678497 chr3 198022430 5617431 0.02836765006873211 0.18513977831529738 chr4 191154276 3241686 0.016958480175457858 0.1470292765388738 chr5 180915260 4951490 0.027369111925660664 0.1800484815529102 chr6 171115067 5662340 0.033090832381230346 0.2314473776624762 chr7 159138663 4148386 0.02606774445503542 0.5094797693581441 chr8 146364022 5152775 0.03520520227300122 0.4272403610502835 chr9 141213431 2758770 0.019536172872961353 0.3013716084015106 chr10 135534747 3647198 0.026909689808178858 0.2834947147512591 chr11 135006516 2620721 0.019411811204727333 0.24367842464276585 chr12 133851895 2911839 0.021754185848470803 0.1619906761166874 chr13 115169878 2758917 0.023955195993174534 0.1656425058072064 chr14 107349540 1852537 0.017257055782446764 0.17486248680051977 chr15 102531392 1509323 0.014720594059622246 0.1344219543516356 chr16 90354753 1874573 0.02074681118324788 0.18151603051842952 chr17 81195210 2066762 0.025454235539263955 0.1965331923797932 chr18 78077248 2504584 0.032078282267325814 0.7023029007387257 chr19 59128983 1595996 0.026991771531061172 0.4472606113886365 chr20 63025520 1498454 0.023775353221996424 0.19153875445149163 chr21 48129895 1681628 0.0349393656478993 0.20701559703745126 chr22 51304566 1183507 0.023068258680913507 0.16440859186945028 chrMT 16571 56732 3.4235712992577394 2.9716913130610254 chrX 155270560 2452371 0.015794178883620953 0.18745730589645282 chrY 59373566 168613 0.002839866481996382 0.08179108628629522