BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084340.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 = 2,330,484 number of mapped reads = 2,101,541 (90.18%) number of supplementary alignments = 15,464 (0.66%) number of secondary alignments = 0 number of mapped bases = 137,850,768 bp number of sequenced bases = 137,803,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,430 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6265 >>>>>>> ACTG content number of A's = 37,915,132 bp (27.51%) number of C's = 26,524,623 bp (19.25%) number of T's = 41,871,890 bp (30.39%) number of G's = 31,325,848 bp (22.73%) number of N's = 165,993 bp (0.12%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,359,576 number of insertions = 10,477 mapped reads with insertion percentage = 0.49% number of deletions = 29,235 mapped reads with deletion percentage = 1.38% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.0445X std coverageData = 0.3145X There is a 3.85% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% 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% of reference with a coverageData >= 6X There is a 0% 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 13792915 0.05533753514700371 0.5351114643442169 chr2 243199373 13563846 0.05577253688067691 0.3748122528929852 chr3 198022430 9427275 0.047607106932280346 0.24816895236806127 chr4 191154276 6535096 0.03418754807242711 0.2161085757304733 chr5 180915260 7245033 0.040046555497861264 0.22409295821838454 chr6 171115067 6675981 0.03901457140533393 0.24277007889885416 chr7 159138663 7641305 0.048016646966551425 0.3785333751193704 chr8 146364022 6834077 0.046692328528659864 0.2917447971296965 chr9 141213431 4999126 0.03540120769390555 0.24775119709530177 chr10 135534747 10348128 0.07635036940010667 0.48616074716634866 chr11 135006516 7772815 0.05757362852027083 0.308945787502667 chr12 133851895 4903368 0.036632787305700826 0.21592805913323085 chr13 115169878 3434036 0.029817136734311727 0.19371194444337173 chr14 107349540 3719935 0.034652547183714064 0.21593624279042797 chr15 102531392 3031234 0.029563960274722495 0.20111032307376572 chr16 90354753 3152517 0.03489043902316904 0.2273198205076227 chr17 81195210 3866006 0.04761372007043273 0.2540093588033091 chr18 78077248 3766581 0.04824172337631572 0.3912738581723001 chr19 59128983 3085729 0.05218640408545501 0.4008058099484897 chr20 63025520 2816722 0.04469176930233975 0.23934061810097487 chr21 48129895 1581628 0.03286165490284157 0.20982523237545464 chr22 51304566 1100571 0.02145171640278567 0.1645176962639645 chrMT 16571 12584 0.7593989499728441 1.2279734814452656 chrX 155270560 8250893 0.053138811375446834 0.27869851209819974 chrY 59373566 293367 0.0049410372285875505 0.10748780850095327