BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504737.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,138,983 number of mapped reads = 1,905,457 (89.08%) number of secondary alignments = 0 number of mapped bases = 60,968,554 bp number of sequenced bases = 60,968,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,394 duplication rate = 4.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.1246 >>>>>>> ACTG content number of A's = 17,543,354 bp (28.77%) number of C's = 12,307,442 bp (20.19%) number of T's = 18,684,587 bp (30.65%) number of G's = 12,433,056 bp (20.39%) number of N's = 115 bp (0%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 31,131 >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.5032X There is a 1.36% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.04% 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 0.02% 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% 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 5078074 0.02037336548902721 0.22548936166978278 chr2 243199373 4143884 0.017039040639302963 0.17719425435634575 chr3 198022430 6052200 0.030563204380433064 1.1252871438541 chr4 191154276 4565004 0.02388125495032086 0.41302207931864 chr5 180915260 4030074 0.0222760313309115 0.25977510953715743 chr6 171115067 4363588 0.02550089876071521 0.3745636753643759 chr7 159138663 3865944 0.024292927482996385 1.2738910353280808 chr8 146364022 3004912 0.020530400565242735 0.46455344885484484 chr9 141213431 2752256 0.019490044116271064 0.4299547174610039 chr10 135534747 2855910 0.021071423108938996 0.4038670671768446 chr11 135006516 2434564 0.018032937017647355 0.19051841842964196 chr12 133851895 2941938 0.02197905378926462 0.24383887088551845 chr13 115169878 1804394 0.015667238963299066 0.24613577800308237 chr14 107349540 2182500 0.02033078111000755 0.6168681594565057 chr15 102531392 2140732 0.0208787958325973 0.30103592311578503 chr16 90354753 1386546 0.015345578997930523 0.17509074055747995 chr17 81195210 1546806 0.01905045876474733 0.47025881031493605 chr18 78077248 1343102 0.01720222003726361 0.2148630280256381 chr19 59128983 689714 0.011664567273210162 0.1290890779831941 chr20 63025520 1391814 0.02208334020885508 0.27625133898048404 chr21 48129895 601488 0.0124971808062328 0.13392917639722046 chr22 51304566 420494 0.008196034637540837 0.23080857843997635 chrMT 16571 0 0.0 0.0 chrX 155270560 793830 0.0051125596507155 0.08281483099774255 chrY 59373566 578786 0.009748210171509657 0.13502661054734108