BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231755.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 = 4,251,616 number of mapped reads = 3,361,979 (79.08%) number of supplementary alignments = 36,427 (0.86%) number of secondary alignments = 0 number of mapped bases = 230,852,328 bp number of sequenced bases = 230,780,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 932,918 duplication rate = 11.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3072 >>>>>>> ACTG content number of A's = 55,948,367 bp (24.24%) number of C's = 38,437,616 bp (16.66%) number of T's = 59,975,714 bp (25.99%) number of G's = 76,370,336 bp (33.09%) number of N's = 48,460 bp (0.02%) GC percentage = 49.75% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,401,314 number of insertions = 14,735 mapped reads with insertion percentage = 0.43% number of deletions = 43,811 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.0746X std coverageData = 67.5019X There is a 2.06% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 17266339 0.0692730029346647 0.7745160916215684 chr2 243199373 65226085 0.26820005411773823 240.82060606776182 chr3 198022430 13515970 0.06825474265718283 0.6205711253226869 chr4 191154276 3226624 0.016879685181617386 0.33813413620559474 chr5 180915260 2393851 0.01323189099692309 0.2419716111436057 chr6 171115067 12438850 0.07269289734725698 0.721329894808192 chr7 159138663 3058473 0.01921891853521479 0.4299672690443721 chr8 146364022 11335049 0.07744423011278004 0.9536413338557617 chr9 141213431 2005454 0.014201581151299977 0.40771750960725217 chr10 135534747 2153509 0.01588898085300591 0.8350219689264151 chr11 135006516 23589960 0.17473201071272737 1.0682991948645035 chr12 133851895 23749684 0.17743255708109326 1.032144867476479 chr13 115169878 1388361 0.012054896854193073 0.25166488324356423 chr14 107349540 6014739 0.0560294808901836 0.6617237600821616 chr15 102531392 1121035 0.01093357827425185 0.26864482975951937 chr16 90354753 7620663 0.08434158411124205 0.7166316516543748 chr17 81195210 1037274 0.012775063947737805 0.2683124100635414 chr18 78077248 3571971 0.04574919187725469 0.6635023023989498 chr19 59128983 3296578 0.05575232031303498 0.835219688912498 chr20 63025520 11774290 0.18681781602119268 1.1102942169529937 chr21 48129895 8978130 0.18653957171525098 1.0875385961208421 chr22 51304566 2458081 0.04791154455921136 0.5071635475661278 chrMT 16571 120595 7.277472693259308 8.07451662522155 chrX 155270560 3032992 0.019533593489970025 0.3261931001124796 chrY 59373566 477771 0.008046863818150993 0.2043782134346068