BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926921.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 30,402,640 number of mapped reads = 29,456,945 (96.89%) number of supplementary alignments = 1,019,379 (3.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,777,454 number of mapped paired reads (second in pair) = 14,679,491 number of mapped paired reads (both in pair) = 29,032,368 number of mapped paired reads (singletons) = 424,577 number of mapped bases = 2,690,684,281 bp number of sequenced bases = 2,688,561,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,785,223 duplication rate = 7.45% >>>>>>> Insert size mean insert size = 376,698.9948 std insert size = 6,023,847.5267 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 52.4362 >>>>>>> ACTG content number of A's = 758,886,525 bp (28.23%) number of C's = 533,663,733 bp (19.85%) number of T's = 766,672,081 bp (28.52%) number of G's = 629,112,787 bp (23.4%) number of N's = 226,708 bp (0.01%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 25,629,654 number of insertions = 459,244 mapped reads with insertion percentage = 1.53% number of deletions = 1,444,830 mapped reads with deletion percentage = 4.78% homopolymer indels = 51.93% >>>>>>> Coverage mean coverageData = 0.8692X std coverageData = 3.3808X There is a 34.02% of reference with a coverageData >= 1X There is a 18.91% of reference with a coverageData >= 2X There is a 10.98% of reference with a coverageData >= 3X There is a 6.87% of reference with a coverageData >= 4X There is a 4.46% of reference with a coverageData >= 5X There is a 2.99% of reference with a coverageData >= 6X There is a 2.05% of reference with a coverageData >= 7X There is a 1.44% of reference with a coverageData >= 8X There is a 1.02% of reference with a coverageData >= 9X There is a 0.74% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% 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 0.02% 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 222969794 0.8945606358188372 2.7306002796546416 chr2 243199373 231146631 0.9504409001909722 4.506773598178911 chr3 198022430 180614410 0.9120906656887303 1.957506843644047 chr4 191154276 158651174 0.8299640338675971 2.0971538939071537 chr5 180915260 161128795 0.8906313099293006 1.8550728256179796 chr6 171115067 153501409 0.8970654173895745 2.17040097417439 chr7 159138663 137971596 0.8669897899041668 2.2702661373162423 chr8 146364022 135058512 0.9227575886101299 2.0426888000275567 chr9 141213431 114011360 0.8073690950827475 3.11957119795108 chr10 135534747 135790101 1.0018840482286067 10.592705532337225 chr11 135006516 128798731 0.9540186267750217 2.4104005766741903 chr12 133851895 121987668 0.9113630255290746 2.2314254380438907 chr13 115169878 79569603 0.6908890100586891 1.6910981665555567 chr14 107349540 80104372 0.7462013530751972 1.7524128298792212 chr15 102531392 81100481 0.7909819560432769 1.8685550019398276 chr16 90354753 86495454 0.9572872608040885 4.607961265314026 chr17 81195210 72445708 0.8922411556051151 2.085550551291464 chr18 78077248 70162927 0.8986347341545645 3.123423168256843 chr19 59128983 46788375 0.791293416969475 2.1155913891892917 chr20 63025520 64363571 1.0212303048035145 2.1749033739774664 chr21 48129895 34195118 0.7104756409711677 2.5259075678803224 chr22 51304566 36634138 0.7140521956661713 1.8720473519308558 chrMT 16571 1238061 74.7125098062881 49.58655788198994 chrX 155270560 151847898 0.9779567871720176 2.057493730770872 chrY 59373566 4108394 0.06919567539534344 1.5714556358918004