BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231833.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 = 4,682,739 number of mapped reads = 4,342,405 (92.73%) number of supplementary alignments = 17,216 (0.37%) number of secondary alignments = 0 number of mapped bases = 275,508,630 bp number of sequenced bases = 275,404,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 385,298 duplication rate = 6.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8339 >>>>>>> ACTG content number of A's = 69,819,293 bp (25.35%) number of C's = 49,330,654 bp (17.91%) number of T's = 89,361,143 bp (32.45%) number of G's = 66,790,426 bp (24.25%) number of N's = 102,628 bp (0.04%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,706,450 number of insertions = 18,291 mapped reads with insertion percentage = 0.42% number of deletions = 57,876 mapped reads with deletion percentage = 1.32% homopolymer indels = 44.82% >>>>>>> Coverage mean coverageData = 0.089X std coverageData = 0.9777X There is a 6.99% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 25719523 0.10318739787613207 2.110706540433276 chr2 243199373 20119801 0.0827296581887158 1.039515072107018 chr3 198022430 31475051 0.15894689808624204 0.49626274848308094 chr4 191154276 8561473 0.04478828922456331 0.3515426122722759 chr5 180915260 15518592 0.08577823672806816 0.3694251345257366 chr6 171115067 20410466 0.11927918656046811 0.7510084912371723 chr7 159138663 19096876 0.12000148574831246 1.815689431368869 chr8 146364022 13900286 0.09497064790963451 0.7582148625877783 chr9 141213431 14205428 0.10059544548563515 0.7794449522791038 chr10 135534747 9133642 0.0673896709306581 0.813392877939769 chr11 135006516 10886805 0.0806391078190626 0.7288453424648406 chr12 133851895 7743861 0.05785395118985801 0.34565676514429533 chr13 115169878 9351626 0.0811985404725357 0.35607005929048885 chr14 107349540 11224311 0.10455853839709048 0.4804568379880326 chr15 102531392 6655643 0.06491322189403222 0.36588209462546 chr16 90354753 6184756 0.06844970291712268 0.44291748711583984 chr17 81195210 5631831 0.06936161628253687 0.42836572826403735 chr18 78077248 6967914 0.089243847324127 1.8475310187049423 chr19 59128983 5430309 0.09183836292262967 1.2265794415534572 chr20 63025520 5249753 0.08329567134075212 0.43525611752584537 chr21 48129895 5717569 0.11879454546908944 0.4810811616584216 chr22 51304566 1972144 0.03843993144781695 0.23139567309510095 chrMT 16571 207451 12.518918592722226 7.659366392237475 chrX 155270560 13381446 0.08618147574144126 0.5221015743321397 chrY 59373566 762073 0.012835223675128423 0.2822698479067602