BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514711.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 95,060,582 number of mapped reads = 94,216,975 (99.11%) number of supplementary alignments = 5,085,172 (5.35%) number of secondary alignments = 0 number of mapped bases = 8,978,690,017 bp number of sequenced bases = 8,967,880,761 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,130,897 duplication rate = 40.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.6411 >>>>>>> ACTG content number of A's = 2,548,668,676 bp (28.42%) number of C's = 1,930,456,026 bp (21.53%) number of T's = 2,525,180,439 bp (28.16%) number of G's = 1,956,519,868 bp (21.82%) number of N's = 7,055,752 bp (0.08%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 71,177,957 number of insertions = 3,281,279 mapped reads with insertion percentage = 3.37% number of deletions = 3,721,847 mapped reads with deletion percentage = 3.76% homopolymer indels = 36.09% >>>>>>> Coverage mean coverageData = 2.9004X std coverageData = 253.5699X There is a 10.85% of reference with a coverageData >= 1X There is a 7.4% of reference with a coverageData >= 2X There is a 5.99% of reference with a coverageData >= 3X There is a 5.26% of reference with a coverageData >= 4X There is a 4.77% of reference with a coverageData >= 5X There is a 4.42% of reference with a coverageData >= 6X There is a 4.15% of reference with a coverageData >= 7X There is a 3.92% of reference with a coverageData >= 8X There is a 3.73% of reference with a coverageData >= 9X There is a 3.56% of reference with a coverageData >= 10X There is a 3.41% of reference with a coverageData >= 11X There is a 3.28% of reference with a coverageData >= 12X There is a 3.16% of reference with a coverageData >= 13X There is a 3.04% of reference with a coverageData >= 14X There is a 2.94% of reference with a coverageData >= 15X There is a 2.84% of reference with a coverageData >= 16X There is a 2.75% of reference with a coverageData >= 17X There is a 2.67% of reference with a coverageData >= 18X There is a 2.59% of reference with a coverageData >= 19X There is a 2.51% of reference with a coverageData >= 20X There is a 2.44% of reference with a coverageData >= 21X There is a 2.38% of reference with a coverageData >= 22X There is a 2.31% of reference with a coverageData >= 23X There is a 2.25% of reference with a coverageData >= 24X There is a 2.19% of reference with a coverageData >= 25X There is a 2.13% of reference with a coverageData >= 26X There is a 2.08% of reference with a coverageData >= 27X There is a 2.03% of reference with a coverageData >= 28X There is a 1.98% of reference with a coverageData >= 29X There is a 1.93% of reference with a coverageData >= 30X There is a 1.89% of reference with a coverageData >= 31X There is a 1.85% of reference with a coverageData >= 32X There is a 1.8% of reference with a coverageData >= 33X There is a 1.76% of reference with a coverageData >= 34X There is a 1.73% of reference with a coverageData >= 35X There is a 1.69% of reference with a coverageData >= 36X There is a 1.65% of reference with a coverageData >= 37X There is a 1.62% of reference with a coverageData >= 38X There is a 1.58% of reference with a coverageData >= 39X There is a 1.55% of reference with a coverageData >= 40X There is a 1.52% of reference with a coverageData >= 41X There is a 1.49% of reference with a coverageData >= 42X There is a 1.46% of reference with a coverageData >= 43X There is a 1.43% of reference with a coverageData >= 44X There is a 1.4% of reference with a coverageData >= 45X There is a 1.38% of reference with a coverageData >= 46X There is a 1.35% of reference with a coverageData >= 47X There is a 1.33% of reference with a coverageData >= 48X There is a 1.3% of reference with a coverageData >= 49X There is a 1.28% of reference with a coverageData >= 50X There is a 1.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 619415019 2.485109230680713 25.60340322683764 chr2 243199373 753188678 3.09700090386335 84.38549526199822 chr3 198022430 416889860 2.1052658529642323 22.222613678488322 chr4 191154276 536277958 2.8054719424638974 24.18394973671431 chr5 180915260 1012451323 5.596273763749946 930.0115312562302 chr6 171115067 486686652 2.8442068868196158 24.762663783951773 chr7 159138663 489201653 3.074059086445888 48.55767254942291 chr8 146364022 531910387 3.634160770739137 43.1433270058803 chr9 141213431 432405513 3.0620707247032333 103.25696805997542 chr10 135534747 382990375 2.8257726042754188 30.679988285424077 chr11 135006516 531357163 3.9357890177685944 56.00922910714805 chr12 133851895 363441330 2.7152497915700033 36.11941811920833 chr13 115169878 142955995 1.2412620164449597 17.242375931230367 chr14 107349540 244795186 2.280356171065102 24.48016575000465 chr15 102531392 258285162 2.5190837358377034 23.94495914496172 chr16 90354753 658260072 7.285284394502191 533.3838967328064 chr17 81195210 144042872 1.7740316454628295 20.84055830646924 chr18 78077248 155857354 1.9961942562319819 30.569264282198713 chr19 59128983 351532158 5.945175109810362 432.18336685582835 chr20 63025520 171079194 2.714443196977986 54.46949322480433 chr21 48129895 101747395 2.114016558731325 61.80643097302406 chr22 51304566 47657119 0.9289059963980594 15.618433606508184 chrMT 16571 3747445 226.14477098545652 133.04822597079618 chrX 155270560 117265000 0.7552300964200812 20.979016171985748 chrY 59373566 25249154 0.4252591801543468 9.675522652068127