BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234031.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 = 2,656,825 number of mapped reads = 2,184,233 (82.21%) number of supplementary alignments = 10,564 (0.4%) number of secondary alignments = 0 number of mapped bases = 141,135,467 bp number of sequenced bases = 141,079,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,868 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8952 >>>>>>> ACTG content number of A's = 37,602,323 bp (26.65%) number of C's = 26,984,256 bp (19.13%) number of T's = 43,226,461 bp (30.64%) number of G's = 33,242,015 bp (23.56%) number of N's = 24,835 bp (0.02%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,046,629 number of insertions = 9,604 mapped reads with insertion percentage = 0.43% number of deletions = 31,796 mapped reads with deletion percentage = 1.44% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.0456X std coverageData = 0.3838X There is a 3.76% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 15865658 0.06365343418743177 0.6050958842207574 chr2 243199373 4969650 0.02043446880103593 0.4068754839256589 chr3 198022430 13033594 0.06581877618611184 0.30058588792375246 chr4 191154276 4620540 0.024171784679302703 0.20418575438233935 chr5 180915260 7500347 0.04145779079111403 0.23665925063498022 chr6 171115067 11462843 0.06698909219957819 0.41070007305787704 chr7 159138663 9580162 0.060200091036331005 0.6503768557067823 chr8 146364022 8802785 0.06014309308881933 0.3770035755532761 chr9 141213431 5989150 0.0424120422369739 0.3504787758112143 chr10 135534747 6363822 0.046953435490605225 0.3939222563610963 chr11 135006516 5696949 0.042197585485429456 0.3281548597313647 chr12 133851895 4002601 0.029903207571323514 0.20941854903825988 chr13 115169878 5549957 0.048189310402846824 0.2568258007486135 chr14 107349540 7155888 0.0666596987746757 0.3301621582952952 chr15 102531392 2118655 0.020663476411204872 0.16807845047925685 chr16 90354753 3468285 0.03838519706871425 0.2799223150732756 chr17 81195210 3502352 0.04313495833067 0.26951477235236215 chr18 78077248 2039748 0.026124742511416384 0.6800231709221939 chr19 59128983 4347590 0.07352722437319782 0.48960453862432707 chr20 63025520 4052588 0.064300746745128 0.3074099519846787 chr21 48129895 2905598 0.060369921854182315 0.3131682523578022 chr22 51304566 1712810 0.0333851376893043 0.21269302896232162 chrMT 16571 152996 9.23275601955223 6.515686703784138 chrX 155270560 5882920 0.037888186917082026 0.25579939402064256 chrY 59373566 357979 0.006029265616284527 0.1347217789786506