BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472785.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,170,014 number of mapped reads = 13,070,941 (99.25%) number of supplementary alignments = 52,020 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,553,218 number of mapped paired reads (second in pair) = 6,517,723 number of mapped paired reads (both in pair) = 13,010,544 number of mapped paired reads (singletons) = 60,397 number of mapped bases = 1,286,200,905 bp number of sequenced bases = 1,286,018,494 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,956,147 duplication rate = 46.42% >>>>>>> Insert size mean insert size = 23,497.7464 std insert size = 1,481,821.173 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.1802 >>>>>>> ACTG content number of A's = 353,303,592 bp (27.47%) number of C's = 291,336,784 bp (22.65%) number of T's = 350,687,498 bp (27.27%) number of G's = 290,441,617 bp (22.58%) number of N's = 249,003 bp (0.02%) GC percentage = 45.24% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 7,675,182 number of insertions = 79,996 mapped reads with insertion percentage = 0.6% number of deletions = 73,024 mapped reads with deletion percentage = 0.55% homopolymer indels = 45.44% >>>>>>> Coverage mean coverageData = 0.4155X std coverageData = 14.9567X There is a 3.67% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 141137102 0.5662457386615699 20.806740283527215 chr2 243199373 87950232 0.36163839945426174 15.916287111986778 chr3 198022430 138799096 0.7009261324588331 16.585222827777685 chr4 191154276 50928095 0.2664240427454524 11.66361367138857 chr5 180915260 59572306 0.329282925055631 10.35965538235496 chr6 171115067 82194472 0.48034619885343 14.317712191643817 chr7 159138663 60667703 0.38122541597575194 15.732826644959351 chr8 146364022 50545891 0.3453436869888694 10.567697111363849 chr9 141213431 74971881 0.5309118294845481 14.862779559074067 chr10 135534747 40336197 0.2976077935202845 11.20371714454665 chr11 135006516 59760084 0.4426459238456313 17.784551882374522 chr12 133851895 61868135 0.4622133664973514 13.02820996509674 chr13 115169878 22577403 0.19603565960189695 9.88863092371526 chr14 107349540 26899324 0.25057698430752473 10.870322279779055 chr15 102531392 42331633 0.4128650959893337 16.411900380758414 chr16 90354753 47797909 0.529002707804425 15.106518124412181 chr17 81195210 60682920 0.7473706884925847 23.03673039525153 chr18 78077248 33552375 0.42973306384979143 18.30079344289908 chr19 59128983 24700221 0.4177345820407566 10.767732381638119 chr20 63025520 38147443 0.6052697859533726 24.85869876641586 chr21 48129895 5088125 0.1057165198469683 4.4283847728199985 chr22 51304566 13211433 0.2575098871316834 9.093258319702812 chrMT 16571 1053 0.06354474684690121 0.2871209493178024 chrX 155270560 60440686 0.38926043674988997 12.946703796744156 chrY 59373566 2039186 0.034345014749493065 1.642074286293075