BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472487.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 = 19,672,406 number of mapped reads = 19,353,746 (98.38%) number of supplementary alignments = 92,833 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,724,122 number of mapped paired reads (second in pair) = 9,629,624 number of mapped paired reads (both in pair) = 19,200,628 number of mapped paired reads (singletons) = 153,118 number of mapped bases = 1,904,747,124 bp number of sequenced bases = 1,904,518,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,933,396 duplication rate = 45.48% >>>>>>> Insert size mean insert size = 34,521.3223 std insert size = 1,813,586.5532 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 55.0936 >>>>>>> ACTG content number of A's = 524,067,665 bp (27.52%) number of C's = 431,174,114 bp (22.64%) number of T's = 520,287,223 bp (27.32%) number of G's = 428,695,800 bp (22.51%) number of N's = 293,343 bp (0.02%) GC percentage = 45.15% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 12,087,613 number of insertions = 110,068 mapped reads with insertion percentage = 0.56% number of deletions = 106,608 mapped reads with deletion percentage = 0.55% homopolymer indels = 42.08% >>>>>>> Coverage mean coverageData = 0.6153X std coverageData = 26.0078X There is a 5.68% of reference with a coverageData >= 1X There is a 2.65% of reference with a coverageData >= 2X There is a 1.22% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.48% 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 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 247377866 0.9924864580377515 43.36700720738431 chr2 243199373 140488893 0.5776696348637379 24.83903257678611 chr3 198022430 214325080 1.0823272898933722 27.93946112859915 chr4 191154276 99863117 0.5224215701039301 38.530161098850265 chr5 180915260 96973052 0.5360136673932315 20.50869206893511 chr6 171115067 135584893 0.7923609263467138 25.65913712830966 chr7 159138663 78947580 0.49609302046228704 20.528708149388507 chr8 146364022 89925282 0.6143947178494452 24.25984687835568 chr9 141213431 109952848 0.7786288260356764 28.680056926020768 chr10 135534747 56941810 0.4201270246957409 17.561938290451607 chr11 135006516 78114415 0.5785973693299367 21.799562638218458 chr12 133851895 103100113 0.7702551614977136 29.110153640571344 chr13 115169878 31640569 0.2747295521143124 11.755580659372542 chr14 107349540 34272773 0.31926334290766406 10.750608649248036 chr15 102531392 58072597 0.5663884578880973 20.88386225706854 chr16 90354753 50248086 0.5561200084294403 14.59287471742271 chr17 81195210 54948108 0.6767407584757771 21.300399991237903 chr18 78077248 34128115 0.4371070430146308 28.750390453510448 chr19 59128983 49061561 0.8297379476322128 36.12156944938015 chr20 63025520 29029859 0.46060483118584344 19.425797701270486 chr21 48129895 7403640 0.15382622380539163 5.62513443084312 chr22 51304566 11773120 0.22947509194405816 6.7486884615048925 chrMT 16571 7037 0.4246575342465753 1.2515040555172499 chrX 155270560 90398941 0.5822027111900672 19.74922235952751 chrY 59373566 2167769 0.036510675474671676 1.197494310835767