BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081942.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,015,011 number of mapped reads = 2,789,444 (92.52%) number of supplementary alignments = 17,332 (0.57%) number of secondary alignments = 0 number of mapped bases = 194,271,556 bp number of sequenced bases = 194,187,281 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,485 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6736 >>>>>>> ACTG content number of A's = 56,528,258 bp (29.11%) number of C's = 36,193,150 bp (18.64%) number of T's = 61,003,576 bp (31.41%) number of G's = 40,436,529 bp (20.82%) number of N's = 25,768 bp (0.01%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,535,541 number of insertions = 14,344 mapped reads with insertion percentage = 0.51% number of deletions = 47,994 mapped reads with deletion percentage = 1.7% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.0628X std coverageData = 0.6248X There is a 5.35% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17887313 0.07176436683782625 1.28353764268139 chr2 243199373 17192838 0.07069441745641343 0.7618749579404157 chr3 198022430 12562976 0.06344218682701752 0.28636465293312474 chr4 191154276 10209233 0.053408342275325295 0.28027399205805426 chr5 180915260 9771529 0.054011635060525025 0.2664796532134627 chr6 171115067 17077778 0.09980288877776029 0.4950892343369639 chr7 159138663 12680130 0.07967975701794101 0.839089664190295 chr8 146364022 10972695 0.07496852607671577 0.9103156263404754 chr9 141213431 9606286 0.06802671624061028 0.6142133397462861 chr10 135534747 7874368 0.05809851845593514 0.6224847957637579 chr11 135006516 8602650 0.06372025776889169 0.4189121108772654 chr12 133851895 8289855 0.06193304173990215 0.29981966820331374 chr13 115169878 5454111 0.04735709627130108 0.24161583081557278 chr14 107349540 4939306 0.04601143144162518 0.2877893483396903 chr15 102531392 4413897 0.04304922535334349 0.23308697489354446 chr16 90354753 4070586 0.04505115519490159 0.3265846923195645 chr17 81195210 5095391 0.0627548226059148 0.33385214363256943 chr18 78077248 5672943 0.07265808087908017 0.9855182452764646 chr19 59128983 3873254 0.06550516859050325 0.8887525881069633 chr20 63025520 4747134 0.07532082242240921 0.31918124306271073 chr21 48129895 2101301 0.04365895666300539 0.286800348919207 chr22 51304566 1441305 0.028093113583691556 0.18317480739523237 chrMT 16571 30294 1.8281334862108503 1.7079615545296356 chrX 155270560 9291945 0.05984357240677177 0.3460592224811968 chrY 59373566 412438 0.00694649197927576 0.17432664574039042