BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524967.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 = 1,107,823 number of mapped reads = 1,017,711 (91.87%) number of supplementary alignments = 3,608 (0.33%) number of secondary alignments = 0 number of mapped bases = 58,747,052 bp number of sequenced bases = 58,731,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,173 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0185 >>>>>>> ACTG content number of A's = 14,799,518 bp (25.2%) number of C's = 11,057,338 bp (18.83%) number of T's = 18,712,290 bp (31.86%) number of G's = 14,160,555 bp (24.11%) number of N's = 1,772 bp (0%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 279,591 number of insertions = 3,894 mapped reads with insertion percentage = 0.38% number of deletions = 9,404 mapped reads with deletion percentage = 0.92% homopolymer indels = 41.66% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.1912X There is a 1.76% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4186127 0.016794850834092805 0.300125569406769 chr2 243199373 4939041 0.020308609101553892 0.20761214483364926 chr3 198022430 3484481 0.017596395519436862 0.13918357179376833 chr4 191154276 3587654 0.018768369063321397 0.15757305956843676 chr5 180915260 3226574 0.017834725495240147 0.14137797412900055 chr6 171115067 3040111 0.017766471727472134 0.14692865489826312 chr7 159138663 3717153 0.023357950418371933 0.24708136853809823 chr8 146364022 2538255 0.017342069214249932 0.17591288357486845 chr9 141213431 2704922 0.019154849371232966 0.20353290523255851 chr10 135534747 2369767 0.0174845716869933 0.19192660633451614 chr11 135006516 2287093 0.016940611962758895 0.16453703545210077 chr12 133851895 4390090 0.032798116156667036 0.2046516165141698 chr13 115169878 2160728 0.018761225048792705 0.14326820980626415 chr14 107349540 2079014 0.019366771389984532 0.15419483336758513 chr15 102531392 1516575 0.014791323617258606 0.1276848212036527 chr16 90354753 1661795 0.018391893562035414 0.14920395408645545 chr17 81195210 1767313 0.021766222416322343 0.15883582232958343 chr18 78077248 1849408 0.023686900439933538 0.32461671771850115 chr19 59128983 998705 0.016890278664187408 0.2241585567477749 chr20 63025520 1747098 0.02772048528913367 0.17846289781024938 chr21 48129895 698456 0.014511895361500373 0.13871390456859914 chr22 51304566 573504 0.011178420259904353 0.11036537512794352 chrMT 16571 9443 0.5698509444209764 0.8636504133187849 chrX 155270560 3048302 0.019632195568818712 0.16263134301409413 chrY 59373566 165443 0.00278647571884094 0.07715041534778738