BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237599.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 = 2,737,080 number of mapped reads = 2,107,785 (77.01%) number of supplementary alignments = 10,518 (0.38%) number of secondary alignments = 0 number of mapped bases = 130,738,411 bp number of sequenced bases = 130,653,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,657 duplication rate = 5.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.006 >>>>>>> ACTG content number of A's = 34,911,065 bp (26.72%) number of C's = 22,595,344 bp (17.29%) number of T's = 41,807,595 bp (32%) number of G's = 31,104,316 bp (23.81%) number of N's = 235,581 bp (0.18%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,357,809 number of insertions = 12,017 mapped reads with insertion percentage = 0.57% number of deletions = 52,492 mapped reads with deletion percentage = 2.46% homopolymer indels = 49.07% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.3909X There is a 3.28% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% 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% 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 11300856 0.045339329365201464 0.5244590828069411 chr2 243199373 11270131 0.0463411186508281 0.556736944412754 chr3 198022430 9627622 0.048618845854987235 0.305671341301243 chr4 191154276 8250040 0.04315906592641433 0.29320120188991056 chr5 180915260 7585696 0.04192955309574217 0.27014830034862103 chr6 171115067 7252348 0.04238287210558729 0.3261578769466045 chr7 159138663 7295423 0.04584318394078754 0.5222497640150053 chr8 146364022 7124730 0.04867815124675926 0.4622658099655474 chr9 141213431 5268015 0.03730533960328462 0.39187872224097187 chr10 135534747 6060105 0.0447125562568837 0.3679923520878563 chr11 135006516 5568445 0.04124574994587669 0.38416886817776963 chr12 133851895 7268897 0.05430552178585144 0.32845071982077945 chr13 115169878 4396840 0.038176996245493984 0.2776265663801306 chr14 107349540 3613602 0.033662016623452695 0.27179688244859457 chr15 102531392 3718437 0.03626632709716845 0.26546729872644026 chr16 90354753 3275995 0.03625703010886434 0.28572624238342353 chr17 81195210 3149394 0.038787928499723075 0.2899878236420593 chr18 78077248 3704417 0.047445537527142354 0.7008465833727877 chr19 59128983 2324610 0.03931422260382865 0.38154150641927975 chr20 63025520 2622221 0.04160570194422831 0.28729655458279124 chr21 48129895 1638682 0.034047071991326804 0.27242815927062347 chr22 51304566 1224850 0.023874093389660483 0.20596114541691987 chrMT 16571 93618 5.64950817693561 4.443489075337483 chrX 155270560 6677916 0.04300825604029508 0.31133870860691504 chrY 59373566 425521 0.007166842564248204 0.16188976994694623