BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714080.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 412,198 number of mapped reads = 299,716 (72.71%) number of supplementary alignments = 11,016 (2.67%) number of secondary alignments = 0 number of mapped bases = 38,428,574 bp number of sequenced bases = 37,689,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 234,916 duplication rate = 42.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.6157 >>>>>>> ACTG content number of A's = 10,349,264 bp (27.46%) number of C's = 8,114,759 bp (21.53%) number of T's = 9,804,122 bp (26.01%) number of G's = 9,420,736 bp (25%) number of N's = 262 bp (0%) GC percentage = 46.53% >>>>>>> Mismatches and indels general error rate = 0.0421 number of mismatches = 1,459,550 number of insertions = 41,322 mapped reads with insertion percentage = 13.35% number of deletions = 127,405 mapped reads with deletion percentage = 40.45% homopolymer indels = 28.54% >>>>>>> Coverage mean coverageData = 0.0124X std coverageData = 1.6152X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3491574 0.01400828606160223 1.471805513750597 chr2 243199373 4191839 0.017236224535825594 3.902002559394377 chr3 198022430 2093046 0.010569742023668734 1.0183395548045353 chr4 191154276 1751203 0.009161202336901948 1.0088843966101029 chr5 180915260 2034587 0.011246077307132632 1.0275741308886701 chr6 171115067 1496859 0.00874767503670498 0.7820421417324649 chr7 159138663 1497209 0.009408203963608768 0.8642184188003289 chr8 146364022 1844389 0.012601382326047312 1.3101368476805242 chr9 141213431 1439994 0.010197287820306555 1.077333205372436 chr10 135534747 2182020 0.01609934019355199 1.464751470511565 chr11 135006516 1770429 0.013113655936429025 1.2149369054324985 chr12 133851895 1601021 0.011961138092217521 1.142132059606722 chr13 115169878 1009811 0.008768013108427536 0.9375130782060167 chr14 107349540 1297533 0.012086991709512681 1.3828172975598596 chr15 102531392 1100199 0.010730362463039612 0.9597197927832362 chr16 90354753 1269316 0.014048137567262234 1.566042582605324 chr17 81195210 1379483 0.016989709122003625 1.6109960492930384 chr18 78077248 849910 0.010885501497183918 0.9399827900091483 chr19 59128983 752213 0.012721561607105605 1.302024910092299 chr20 63025520 1066943 0.016928745689047866 1.4470531212796955 chr21 48129895 278973 0.0057962519968098826 0.48967200015498547 chr22 51304566 490645 0.009563378822851751 1.0635242212617713 chrMT 16571 308731 18.630800796572323 171.5056017835422 chrX 155270560 3086982 0.019881309116164713 1.226392452129812 chrY 59373566 143665 0.00241967949171185 0.3788995643686458