BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237795.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 = 4,120,776 number of mapped reads = 3,597,888 (87.31%) number of supplementary alignments = 36,214 (0.88%) number of secondary alignments = 0 number of mapped bases = 252,369,204 bp number of sequenced bases = 252,234,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 427,888 duplication rate = 9.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6621 >>>>>>> ACTG content number of A's = 76,070,603 bp (30.16%) number of C's = 50,233,264 bp (19.92%) number of T's = 73,940,312 bp (29.31%) number of G's = 51,564,682 bp (20.44%) number of N's = 425,262 bp (0.17%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 2,223,988 number of insertions = 18,320 mapped reads with insertion percentage = 0.5% number of deletions = 75,260 mapped reads with deletion percentage = 2.07% homopolymer indels = 43.73% >>>>>>> Coverage mean coverageData = 0.0815X std coverageData = 1.2851X There is a 1.79% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 22895099 0.09185573503546056 2.83558597560726 chr2 243199373 26138711 0.10747852956018929 1.1801291981290305 chr3 198022430 16498594 0.08331679396116895 0.9880346487781443 chr4 191154276 18068725 0.0945243045465538 1.0579066785835185 chr5 180915260 11062565 0.06114777161418003 0.8460062919678355 chr6 171115067 18035595 0.10540039118822891 1.1561365103714796 chr7 159138663 14145348 0.08888693503727627 1.2576684845026382 chr8 146364022 15577338 0.10642873697471911 1.210385568599188 chr9 141213431 8115062 0.05746664423159579 0.9090094556985368 chr10 135534747 10809847 0.07975701611041484 1.1462929860862667 chr11 135006516 11620605 0.08607440103113245 1.0774844418494285 chr12 133851895 10180003 0.07605423143243507 0.9497225503004983 chr13 115169878 8012317 0.06956955359456055 0.8969785912576147 chr14 107349540 9120350 0.08495937663077084 0.9988261255907087 chr15 102531392 5012315 0.048885662256492136 0.7695726186599172 chr16 90354753 4660213 0.05157684399845573 0.8000496291401841 chr17 81195210 5707820 0.0702974966134086 0.9223479395123927 chr18 78077248 5138771 0.06581649752819156 1.2656767658464239 chr19 59128983 5586187 0.09447459970688148 1.625420087286985 chr20 63025520 3702338 0.058743474072090164 0.8455655001811235 chr21 48129895 3225630 0.06701926110580544 0.9024400569334515 chr22 51304566 2307008 0.04496691386103919 0.7440849154055177 chrMT 16571 63811 3.8507633818115985 5.617983952186113 chrX 155270560 15935740 0.10263207655076403 1.0582215834125426 chrY 59373566 749212 0.012618612127828064 0.3741996256466931