BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085084.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 = 3,043,545 number of mapped reads = 2,738,131 (89.97%) number of supplementary alignments = 29,060 (0.95%) number of secondary alignments = 0 number of mapped bases = 180,820,247 bp number of sequenced bases = 180,749,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,563 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7658 >>>>>>> ACTG content number of A's = 50,695,989 bp (28.05%) number of C's = 34,538,597 bp (19.11%) number of T's = 54,889,501 bp (30.37%) number of G's = 40,601,012 bp (22.46%) number of N's = 24,522 bp (0.01%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,537,969 number of insertions = 14,963 mapped reads with insertion percentage = 0.54% number of deletions = 43,199 mapped reads with deletion percentage = 1.56% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.4861X There is a 4.96% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 15236765 0.061130299049485616 0.919210680210278 chr2 243199373 14044807 0.05775017767007154 0.5773330769173556 chr3 198022430 11556529 0.0583596969292822 0.28343703755030303 chr4 191154276 11922079 0.06236888470127658 0.30805201839014557 chr5 180915260 10729665 0.05930768360833685 0.27762763673638347 chr6 171115067 10889780 0.06364010014384064 0.41404885005873576 chr7 159138663 9480595 0.05957442912537225 0.46389770623250093 chr8 146364022 9089725 0.0621035475507772 0.5851968654162929 chr9 141213431 7630803 0.054037374107849555 0.4185822331109653 chr10 135534747 8323664 0.06141350601407033 0.6448321057206176 chr11 135006516 8543446 0.0632817307869792 0.49335995056504867 chr12 133851895 8462746 0.06322470070371436 0.291161279384214 chr13 115169878 5229289 0.04540500598602701 0.24079135743543478 chr14 107349540 5965384 0.05556972111850689 0.30663215629682006 chr15 102531392 5486068 0.05350622763416691 0.26880068930948237 chr16 90354753 5488660 0.060745669904050316 0.3316540031636409 chr17 81195210 5182321 0.06382545226497967 0.3428305062824709 chr18 78077248 4820065 0.06173456574698944 0.8056595308141126 chr19 59128983 3849597 0.06510507714972875 0.657764532909128 chr20 63025520 3766352 0.05975915787763433 0.29337587580853386 chr21 48129895 2488246 0.051698554505469 0.28862028319200433 chr22 51304566 2174746 0.042388936688403135 0.23296843412449342 chrMT 16571 18566 1.1203910445959808 1.1734954131933957 chrX 155270560 9979146 0.06426940174621641 0.3452556027455036 chrY 59373566 461203 0.0077678170787316364 0.17628724928913386