BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549091.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,410,499 number of mapped reads = 8,272,349 (87.91%) number of secondary alignments = 0 number of mapped bases = 328,255,467 bp number of sequenced bases = 328,223,205 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 354,241 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7969 >>>>>>> ACTG content number of A's = 98,925,279 bp (30.14%) number of C's = 65,233,557 bp (19.87%) number of T's = 100,132,032 bp (30.51%) number of G's = 63,851,305 bp (19.45%) number of N's = 81,032 bp (0.02%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,378,708 number of insertions = 8,407 mapped reads with insertion percentage = 0.1% number of deletions = 25,848 mapped reads with deletion percentage = 0.31% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.106X std coverageData = 1.2602X There is a 8.93% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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% 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 28635701 0.11488718016072666 3.43233905689657 chr2 243199373 31846453 0.13094792394880064 0.8637770312976364 chr3 198022430 25392006 0.1282279285230466 0.42439996032606814 chr4 191154276 26845767 0.14044031638612153 0.44084370096669534 chr5 180915260 18717482 0.1034599403057542 0.40129547132261595 chr6 171115067 20159735 0.11781390939700243 0.5506026029503525 chr7 159138663 19098064 0.12000895093607768 1.3277328706002138 chr8 146364022 12800250 0.08745489379896926 1.1119117469891324 chr9 141213431 11728533 0.08305536461329943 0.8151167152617199 chr10 135534747 13979205 0.10314111553991391 0.9916848299815544 chr11 135006516 13910400 0.1030350268427044 0.7824311070067893 chr12 133851895 13378638 0.09995105411096346 0.4295622153819577 chr13 115169878 12308076 0.10686888111490402 0.36055872247994813 chr14 107349540 10904686 0.10158111529867757 0.46869400023593105 chr15 102531392 9427244 0.09194495281991295 0.3434776299152901 chr16 90354753 9323828 0.10319133958564415 0.5436894710361639 chr17 81195210 5081906 0.06258874138018733 0.3287658566915124 chr18 78077248 10262666 0.1314424658000241 1.7480724056877108 chr19 59128983 5207833 0.08807580877891981 2.762336264166602 chr20 63025520 6153755 0.09763909920933615 0.39594534733103687 chr21 48129895 4601209 0.09559981379556302 0.4482121942929157 chr22 51304566 2919356 0.0569024597147942 0.3482332404828174 chrMT 16571 9489 0.5726268782813349 1.0335477330074614 chrX 155270560 13259459 0.08539583421351736 0.5064513331001644 chrY 59373566 2303726 0.038800532883606825 0.3172380211824861