BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975296.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 3,351,676 number of mapped reads = 3,324,789 (99.2%) number of supplementary alignments = 13,029 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,661,601 number of mapped paired reads (second in pair) = 1,663,188 number of mapped paired reads (both in pair) = 3,313,598 number of mapped paired reads (singletons) = 11,191 number of mapped bases = 303,183,828 bp number of sequenced bases = 303,010,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,252 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 65,874.6877 std insert size = 2,453,257.9146 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 53.0182 >>>>>>> ACTG content number of A's = 89,373,099 bp (29.5%) number of C's = 58,709,474 bp (19.38%) number of T's = 89,717,206 bp (29.61%) number of G's = 65,203,858 bp (21.52%) number of N's = 6,413 bp (0%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 2,484,571 number of insertions = 48,310 mapped reads with insertion percentage = 1.42% number of deletions = 106,503 mapped reads with deletion percentage = 3.14% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.0979X std coverageData = 0.9239X There is a 7.14% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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% 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 25825330 0.10361189832301361 1.0306676782417838 chr2 243199373 26327563 0.108255061167448 0.9471853987469778 chr3 198022430 21147913 0.10679554331294693 0.4203042039308176 chr4 191154276 19800367 0.10358317592644384 0.6272662565784741 chr5 180915260 19032819 0.10520294971247865 0.3993122034382755 chr6 171115067 21695810 0.1267907635509385 0.8225102617982379 chr7 159138663 17059322 0.10719784669800826 1.096252932109163 chr8 146364022 15823800 0.10811263440136948 0.492227128479759 chr9 141213431 12825756 0.090825326664572 1.3804053289896165 chr10 135534747 16355517 0.12067397742661519 2.25939118808626 chr11 135006516 11985732 0.08877891493770568 0.915750299352372 chr12 133851895 13383033 0.09998388890945474 0.39662432709637147 chr13 115169878 10124814 0.08791199726720211 0.36331097574989657 chr14 107349540 8937504 0.08325609965352436 0.39117405082296647 chr15 102531392 8683467 0.08469081352177488 0.36121766794430915 chr16 90354753 9458866 0.10468587081412309 1.2819529325476855 chr17 81195210 6476994 0.0797706416425304 0.9096709097651691 chr18 78077248 8588901 0.11000517077651098 1.4104373966987644 chr19 59128983 3631968 0.061424496342174534 0.6883962475739593 chr20 63025520 6305252 0.10004283978934247 0.41118078345767206 chr21 48129895 3770510 0.07834029141347597 0.4456895666089425 chr22 51304566 2782757 0.054239948155881484 0.2956918445333486 chrMT 16571 45404 2.739967412950335 5.880423110435816 chrX 155270560 9585795 0.06173607540283232 0.4486137272409956 chrY 59373566 3528634 0.059431060617110315 1.1711613280265