BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240046.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 = 1,238,559 number of mapped reads = 1,014,379 (81.9%) number of supplementary alignments = 4,378 (0.35%) number of secondary alignments = 0 number of mapped bases = 63,691,956 bp number of sequenced bases = 63,657,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,884 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7765 >>>>>>> ACTG content number of A's = 17,443,437 bp (27.4%) number of C's = 10,998,291 bp (17.28%) number of T's = 20,558,744 bp (32.3%) number of G's = 14,615,601 bp (22.96%) number of N's = 41,290 bp (0.06%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 614,181 number of insertions = 4,553 mapped reads with insertion percentage = 0.44% number of deletions = 20,343 mapped reads with deletion percentage = 1.98% homopolymer indels = 48.81% >>>>>>> Coverage mean coverageData = 0.0206X std coverageData = 0.2143X There is a 1.8% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4942162 0.01982808299602993 0.29002760201522343 chr2 243199373 5795420 0.02382991341017972 0.2554797760088902 chr3 198022430 4234765 0.021385279435263974 0.16382606640300776 chr4 191154276 4361957 0.022819039632678687 0.17388643371592552 chr5 180915260 3986564 0.022035531994371287 0.1661927410027813 chr6 171115067 3538116 0.020676823274714904 0.18698634487390933 chr7 159138663 4050578 0.025453135797678533 0.3267413272300278 chr8 146364022 3620649 0.02473728823877223 0.32182418003927643 chr9 141213431 1975221 0.013987486785162808 0.18373318528563293 chr10 135534747 3167216 0.02336829536414009 0.19372500184591393 chr11 135006516 2989800 0.02214559777248085 0.210334446927378 chr12 133851895 2856806 0.02134303739218634 0.16516291940561137 chr13 115169878 1538111 0.013355150033240462 0.127884061117563 chr14 107349540 2670935 0.024880730741836436 0.18078738271670952 chr15 102531392 1424381 0.013892145344130313 0.13969694581898165 chr16 90354753 1793097 0.019845076661324058 0.1631997753573333 chr17 81195210 1529641 0.018839054668372678 0.16080485417198687 chr18 78077248 1707562 0.021870161202403034 0.3179350426404246 chr19 59128983 1060068 0.017928060761674185 0.21719974318615587 chr20 63025520 1237197 0.01963009587227523 0.16192139536798797 chr21 48129895 1216615 0.02527774058098402 0.1835472177618006 chr22 51304566 518954 0.010115162069590454 0.10961670041596767 chrMT 16571 20747 1.252006517409933 1.540741479302355 chrX 155270560 3326302 0.02142261868573154 0.17744131167001181 chrY 59373566 129092 0.002174233563805145 0.05621196410437726