BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234079.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 = 2,655,149 number of mapped reads = 1,368,258 (51.53%) number of supplementary alignments = 10,727 (0.4%) number of secondary alignments = 0 number of mapped bases = 86,585,897 bp number of sequenced bases = 86,536,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,446 duplication rate = 7.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0572 >>>>>>> ACTG content number of A's = 24,086,826 bp (27.83%) number of C's = 14,588,506 bp (16.86%) number of T's = 28,877,710 bp (33.37%) number of G's = 18,961,685 bp (21.91%) number of N's = 22,003 bp (0.03%) GC percentage = 38.77% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 835,960 number of insertions = 7,509 mapped reads with insertion percentage = 0.54% number of deletions = 27,921 mapped reads with deletion percentage = 2.01% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.3326X There is a 1.99% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 6254141 0.02509177700303503 0.4522006360152987 chr2 243199373 7069841 0.029070144847782975 0.33542822415147344 chr3 198022430 6711028 0.03389024162565826 0.24999828996435786 chr4 191154276 5925862 0.03100041560147993 0.2531139051324301 chr5 180915260 5245613 0.02899486201440387 0.2352161917838747 chr6 171115067 5452052 0.03186190494844034 0.2708969809694371 chr7 159138663 4679724 0.029406581102167484 0.3128897303964369 chr8 146364022 5257114 0.035918075550014604 0.7845612389412349 chr9 141213431 3470295 0.024574822489795606 0.2887167770293783 chr10 135534747 4436160 0.03273079485661341 0.2952614105369362 chr11 135006516 3843654 0.02847013695250087 0.2676801655145017 chr12 133851895 3539906 0.02644643917816778 0.22916584968632184 chr13 115169878 3265389 0.028352804194166116 0.2367561458161285 chr14 107349540 3125203 0.029112402344714287 0.23847993657241878 chr15 102531392 2039655 0.019892980678541845 0.19396421538403985 chr16 90354753 2111159 0.023365223520670796 0.2077785745559566 chr17 81195210 1915825 0.023595295830874753 0.21676079596228787 chr18 78077248 2328471 0.02982265717152326 0.5296479200876081 chr19 59128983 1506457 0.025477471851663675 0.3207817512648629 chr20 63025520 1920206 0.0304671187163549 0.2408717611834962 chr21 48129895 1254952 0.026074272549316803 0.22162373157373208 chr22 51304566 712212 0.013882039271124523 0.15222570354303405 chrMT 16571 142811 8.618128055035907 7.120374925118005 chrX 155270560 4071271 0.026220495372722297 0.23472716845386493 chrY 59373566 306896 0.005168899573928236 0.12294836782355759