BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238309.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 = 2,370,968 number of mapped reads = 2,140,426 (90.28%) number of supplementary alignments = 16,014 (0.68%) number of secondary alignments = 0 number of mapped bases = 137,944,569 bp number of sequenced bases = 137,871,756 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,712 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8417 >>>>>>> ACTG content number of A's = 37,296,094 bp (27.05%) number of C's = 26,902,815 bp (19.51%) number of T's = 41,241,815 bp (29.91%) number of G's = 32,399,368 bp (23.5%) number of N's = 31,664 bp (0.02%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,207,842 number of insertions = 11,676 mapped reads with insertion percentage = 0.54% number of deletions = 43,485 mapped reads with deletion percentage = 2.01% homopolymer indels = 43.69% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.4218X There is a 3.91% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 10005299 0.04014152085101525 0.9054101748341767 chr2 243199373 11901908 0.04893889261795095 0.5058504410394301 chr3 198022430 8601174 0.043435352247722644 0.2285018283182176 chr4 191154276 6780783 0.035472829286853094 0.25348785337156554 chr5 180915260 9865550 0.054531331408970145 0.2641902304443242 chr6 171115067 7578512 0.04428898128532422 0.2809931373188965 chr7 159138663 5981832 0.03758880392252636 0.3982942284071221 chr8 146364022 6326079 0.04322154388460301 0.43227265079750116 chr9 141213431 7347418 0.052030589073358044 0.4007698565574056 chr10 135534747 5215552 0.03848129070547496 0.38745372796564564 chr11 135006516 6641251 0.04919207751424383 0.334054694107462 chr12 133851895 7891902 0.05895995719746814 0.2743977456619789 chr13 115169878 4622882 0.04013967957837031 0.22041318150087072 chr14 107349540 4003811 0.03729695534792231 0.2616595107870329 chr15 102531392 3743575 0.03651150078992393 0.2244521402267222 chr16 90354753 5447113 0.06028584904659083 0.3097920876107049 chr17 81195210 3738860 0.046047790257578006 0.2540962137417508 chr18 78077248 3814614 0.04885692180134218 0.6771984511944673 chr19 59128983 4547041 0.07690037557385351 0.6184837268892466 chr20 63025520 2349066 0.03727166392280461 0.22495861355324248 chr21 48129895 1490418 0.03096657493227442 0.23818723063515707 chr22 51304566 1736967 0.033855992466635426 0.20430641971203026 chrMT 16571 10369 0.6257316999577576 1.0033298730669329 chrX 155270560 7888252 0.050803268823143295 0.2927963069262435 chrY 59373566 414341 0.006978543279681062 0.20965470302983125