BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818964.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,074,150 number of mapped reads = 2,046,187 (98.65%) number of supplementary alignments = 32,696 (1.58%) number of secondary alignments = 0 number of mapped bases = 189,384,402 bp number of sequenced bases = 189,271,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 941,030 duplication rate = 39.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9889 >>>>>>> ACTG content number of A's = 55,111,845 bp (29.12%) number of C's = 38,783,844 bp (20.49%) number of T's = 53,845,922 bp (28.45%) number of G's = 41,520,667 bp (21.94%) number of N's = 8,925 bp (0%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,160,149 number of insertions = 29,326 mapped reads with insertion percentage = 1.39% number of deletions = 61,233 mapped reads with deletion percentage = 2.93% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.0612X std coverageData = 0.7186X There is a 2.75% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% 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 18909640 0.07586596945730378 1.2848505578799199 chr2 243199373 15335487 0.06305726372082382 1.023895349450231 chr3 198022430 9607774 0.048518614785203876 0.402999692264692 chr4 191154276 10060721 0.05263142007872217 0.48508469391580666 chr5 180915260 10727623 0.05929639655604508 0.4666947158797996 chr6 171115067 7815516 0.045674037576129985 0.4452294945128778 chr7 159138663 9597869 0.06031135878023557 0.7824912716423152 chr8 146364022 17671303 0.12073529244775741 0.7311457521522665 chr9 141213431 8333962 0.05901678006817921 0.6645985045516233 chr10 135534747 10135688 0.07478294846413075 0.8418042282855865 chr11 135006516 5730019 0.0424425366254174 0.4699519437228472 chr12 133851895 8917363 0.06662111881195257 0.48611161789456475 chr13 115169878 4160826 0.03612772777270807 0.34892266920676335 chr14 107349540 4325304 0.04029177954558538 0.39731020917054477 chr15 102531392 5101036 0.049750967976714876 0.413118663775282 chr16 90354753 5773045 0.06389309702390532 0.8202035040583708 chr17 81195210 6801771 0.08377059434910016 0.616098142297443 chr18 78077248 4406049 0.05643191983405973 0.7790342742099361 chr19 59128983 3896680 0.06590135331771223 1.133064186237299 chr20 63025520 5716912 0.09070789102573053 0.6044627590437207 chr21 48129895 2672999 0.0555371874382855 0.47381718895995073 chr22 51304566 1573035 0.030660721308898704 0.35421972133850693 chrMT 16571 102268 6.171504435459537 5.646454915808892 chrX 155270560 11361891 0.07317479243972586 0.5825669082672512 chrY 59373566 649621 0.010941249511609257 0.6776540874514689