BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004148.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 = 4,947,200 number of mapped reads = 4,366,729 (88.27%) number of supplementary alignments = 36,001 (0.73%) number of secondary alignments = 0 number of mapped bases = 298,737,597 bp number of sequenced bases = 298,604,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 289,462 duplication rate = 4.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9914 >>>>>>> ACTG content number of A's = 85,473,940 bp (28.62%) number of C's = 54,464,169 bp (18.24%) number of T's = 96,536,561 bp (32.33%) number of G's = 62,096,207 bp (20.8%) number of N's = 33,422 bp (0.01%) GC percentage = 39.04% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 2,718,292 number of insertions = 26,245 mapped reads with insertion percentage = 0.6% number of deletions = 79,452 mapped reads with deletion percentage = 1.8% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 0.0965X std coverageData = 0.9319X There is a 7.15% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% 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 21931339 0.08798910474931174 1.7216449609121587 chr2 243199373 13474206 0.05540395040409911 0.7912223079172265 chr3 198022430 15988381 0.08074025250573887 0.3602418390798113 chr4 191154276 29248601 0.1530104458662489 0.5460262561750667 chr5 180915260 15964422 0.08824253962877426 0.39041554306386544 chr6 171115067 15282038 0.08930854697909214 0.4254713236272999 chr7 159138663 18904899 0.11879513528400072 1.6120071394323299 chr8 146364022 22984749 0.15703824400234095 1.783772729895396 chr9 141213431 9860366 0.06982597852183055 0.855878428268444 chr10 135534747 19472608 0.14367244142935537 0.8515767672517917 chr11 135006516 9990154 0.07399756912473765 0.5224618785947146 chr12 133851895 14578150 0.1089125409841975 0.45658268774496785 chr13 115169878 7696429 0.06682675308555941 0.3244401326383946 chr14 107349540 6624506 0.06170968222127454 0.41402302425367454 chr15 102531392 6967680 0.06795655324761415 0.3284603877227666 chr16 90354753 8174275 0.09046867739210133 0.5337292483257643 chr17 81195210 7084761 0.08725589846987279 0.40097947916862764 chr18 78077248 9867931 0.1263867676278754 1.7880834592081631 chr19 59128983 5855177 0.09902380698819055 1.1230530273651231 chr20 63025520 4760326 0.07553013445981882 0.3724536243200826 chr21 48129895 4358412 0.09055519443788523 0.4828293785309772 chr22 51304566 3445212 0.06715215172076497 0.31802430031878165 chrMT 16571 378676 22.8517289240239 13.138955541646839 chrX 155270560 24981440 0.16088973981931926 0.6193088233096563 chrY 59373566 862859 0.014532713093230749 0.32203380921635144