BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777266.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 2,736,536 number of mapped reads = 2,644,291 (96.63%) number of supplementary alignments = 42,925 (1.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,328,505 number of mapped paired reads (second in pair) = 1,315,786 number of mapped paired reads (both in pair) = 2,624,238 number of mapped paired reads (singletons) = 20,053 number of mapped bases = 197,935,597 bp number of sequenced bases = 197,900,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,702 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 191,610.7141 std insert size = 4,281,779.3778 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.6787 >>>>>>> ACTG content number of A's = 58,192,704 bp (29.41%) number of C's = 41,127,662 bp (20.78%) number of T's = 57,142,697 bp (28.87%) number of G's = 41,427,001 bp (20.93%) number of N's = 10,548 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,137,153 number of insertions = 41,189 mapped reads with insertion percentage = 1.54% number of deletions = 17,729 mapped reads with deletion percentage = 0.66% homopolymer indels = 49.74% >>>>>>> Coverage mean coverageData = 0.0639X std coverageData = 0.3257X There is a 5.46% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 16789091 0.06735827149654323 0.4370135719584308 chr2 243199373 18675588 0.07679126705643274 0.3238101420693957 chr3 198022430 13610097 0.06873007769877382 0.2924531228855151 chr4 191154276 11877956 0.06213806067304505 0.27885018000166917 chr5 180915260 13263352 0.07331251106180872 0.30149522626912606 chr6 171115067 9475934 0.055377554800595086 0.29568408423137643 chr7 159138663 13132384 0.0825216434047834 0.3434505064312937 chr8 146364022 9878544 0.06749297993464541 0.2943939243505229 chr9 141213431 7220997 0.051135341368484986 0.3235642880764175 chr10 135534747 8975244 0.06622098169408912 0.3517438513149757 chr11 135006516 11681844 0.08652800135957882 0.33749834534033046 chr12 133851895 9298499 0.069468564490626 0.2931370559937903 chr13 115169878 8540411 0.07415490185723736 0.3041694964966776 chr14 107349540 4027114 0.03751403126645908 0.21565173053298345 chr15 102531392 7517176 0.07331584847692305 0.3031607040506445 chr16 90354753 5254968 0.058159286872268914 0.2854990222156771 chr17 81195210 5026031 0.061900585022195274 0.29489293222117496 chr18 78077248 4231500 0.05419632618198838 0.340353820382972 chr19 59128983 3760770 0.06360281894244654 0.33755974669554745 chr20 63025520 5279831 0.08377290659402731 0.3239918721086282 chr21 48129895 1748577 0.03633037221460799 0.22315480012374622 chr22 51304566 1572053 0.0306415807123288 0.19449884169758655 chrMT 16571 647137 39.052380665017196 9.87487023361293 chrX 155270560 6239604 0.04018536417979043 0.22569096751662757 chrY 59373566 210895 0.003552001575920166 0.0953947440073814