BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524457.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 = 2,755,798 number of mapped reads = 2,550,449 (92.55%) number of supplementary alignments = 6,043 (0.22%) number of secondary alignments = 0 number of mapped bases = 148,397,340 bp number of sequenced bases = 148,352,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,817 duplication rate = 4.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2492 >>>>>>> ACTG content number of A's = 38,029,618 bp (25.63%) number of C's = 28,820,163 bp (19.43%) number of T's = 46,227,142 bp (31.16%) number of G's = 35,272,420 bp (23.78%) number of N's = 3,019 bp (0%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 683,470 number of insertions = 8,847 mapped reads with insertion percentage = 0.35% number of deletions = 26,317 mapped reads with deletion percentage = 1.02% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.4104X There is a 4.01% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 14675854 0.05887990947071703 0.7982982001354164 chr2 243199373 11784128 0.04845459860622256 0.46539904183034586 chr3 198022430 8110814 0.04095906711174083 0.23943237121816 chr4 191154276 8405780 0.04397380051283812 0.28379122509149446 chr5 180915260 8081636 0.04467083650102263 0.24802812069337793 chr6 171115067 6355157 0.03713966929633379 0.31016323317831695 chr7 159138663 7229105 0.04542645302983349 0.5337473989136926 chr8 146364022 13764174 0.09404069259588944 0.43200946728035494 chr9 141213431 6358878 0.04503026344569165 0.35797498218955764 chr10 135534747 7814607 0.05765759093496518 0.42135465676184825 chr11 135006516 5004901 0.03707155142052551 0.3716605694132788 chr12 133851895 6918560 0.051688173708709914 0.2681287452654829 chr13 115169878 3265472 0.028353524868716107 0.1969042874830644 chr14 107349540 3528966 0.03287360150774749 0.21909163747389945 chr15 102531392 3886105 0.03790161163519559 0.244107774043418 chr16 90354753 4657513 0.051546961785175816 0.2931540976564544 chr17 81195210 5203723 0.06408903924258587 0.3149659969513271 chr18 78077248 3524175 0.04513702890757625 0.6303834127504554 chr19 59128983 2989476 0.050558556029959116 0.5694002369535913 chr20 63025520 4226932 0.0670669912759149 0.3069718635492402 chr21 48129895 2042255 0.04243215157647861 0.2673494788615878 chr22 51304566 1193823 0.023269332402110175 0.1773718588494388 chrMT 16571 69102 4.17005612214109 3.636686083883371 chrX 155270560 8832533 0.05688478871976761 0.3215077799248108 chrY 59373566 473671 0.007977809518801683 0.2009100758391208