BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472709.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 = 18,596,144 number of mapped reads = 18,396,220 (98.92%) number of supplementary alignments = 64,561 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,234,842 number of mapped paired reads (second in pair) = 9,161,378 number of mapped paired reads (both in pair) = 18,280,986 number of mapped paired reads (singletons) = 115,234 number of mapped bases = 1,811,151,194 bp number of sequenced bases = 1,810,912,525 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,916,811 duplication rate = 47.96% >>>>>>> Insert size mean insert size = 25,118.6364 std insert size = 1,595,847.6166 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 55.2181 >>>>>>> ACTG content number of A's = 491,526,470 bp (27.14%) number of C's = 416,172,252 bp (22.98%) number of T's = 488,383,044 bp (26.97%) number of G's = 414,477,510 bp (22.89%) number of N's = 353,249 bp (0.02%) GC percentage = 45.87% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 11,106,014 number of insertions = 101,438 mapped reads with insertion percentage = 0.55% number of deletions = 96,834 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.5851X std coverageData = 19.7486X There is a 5.03% of reference with a coverageData >= 1X There is a 2.22% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 224284352 0.8998346768411862 30.23665751490239 chr2 243199373 105595875 0.4341946843752759 17.778600681873165 chr3 198022430 178595936 0.9018975072672323 19.787697995718986 chr4 191154276 73444600 0.38421635935572795 18.59054930124759 chr5 180915260 88761222 0.49062319010568817 16.826059427627822 chr6 171115067 117709804 0.6878985355509343 19.79617312465919 chr7 159138663 84660138 0.5319897528610003 20.080470218005836 chr8 146364022 65386971 0.4467421030558999 15.620609184918592 chr9 141213431 126238078 0.8939523465016582 25.357611068809096 chr10 135534747 47280974 0.34884762060315055 15.883918802370678 chr11 135006516 89171087 0.6604946904933092 20.441934451493246 chr12 133851895 99653487 0.7445056119676154 23.910013577155162 chr13 115169878 37110802 0.3222266329048295 13.19924482523972 chr14 107349540 40595950 0.37816603592339565 12.645653622267648 chr15 102531392 31242336 0.30470995653701843 10.094798014553223 chr16 90354753 84478153 0.9349608094219459 26.49966408842801 chr17 81195210 77998983 0.9606352763913044 23.116178317297507 chr18 78077248 36714329 0.4702308283201785 18.049063390663537 chr19 59128983 44847986 0.7584772090532996 18.656208267958007 chr20 63025520 35737929 0.5670390184801332 14.859723234496474 chr21 48129895 6135714 0.12748238906401105 4.140967881400603 chr22 51304566 25020070 0.48767725664027645 14.440820528504464 chrMT 16571 6651 0.4013638283748718 1.3105950093629626 chrX 155270560 88228112 0.5682217672171724 19.100850060789806 chrY 59373566 2251655 0.037923526439358556 1.3897842555859614