BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083762.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 = 2,209,033 number of mapped reads = 1,611,167 (72.94%) number of supplementary alignments = 7,215 (0.33%) number of secondary alignments = 0 number of mapped bases = 102,842,627 bp number of sequenced bases = 102,805,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,175 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3783 >>>>>>> ACTG content number of A's = 29,020,116 bp (28.23%) number of C's = 19,790,413 bp (19.25%) number of T's = 30,037,344 bp (29.22%) number of G's = 23,956,519 bp (23.3%) number of N's = 1,123 bp (0%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 909,684 number of insertions = 7,260 mapped reads with insertion percentage = 0.45% number of deletions = 22,585 mapped reads with deletion percentage = 1.39% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0332X std coverageData = 0.2562X There is a 2.99% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% 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 8047543 0.032286952657181144 0.36019612303162485 chr2 243199373 8420148 0.03462240833984387 0.31889171577992775 chr3 198022430 6725238 0.03396200117330143 0.20076747044629986 chr4 191154276 6543477 0.034231392239428636 0.2105747758512307 chr5 180915260 6256173 0.03458068158540081 0.20208465042434917 chr6 171115067 6042078 0.03531002912794348 0.2332336290266238 chr7 159138663 5635727 0.035413939603099465 0.2836683923031539 chr8 146364022 5184298 0.035420576239699124 0.25400308826252116 chr9 141213431 4425587 0.031339703090989976 0.2515628937263438 chr10 135534747 4783588 0.03529418179383918 0.26755358295320075 chr11 135006516 4796713 0.035529492517235244 0.24575452727166236 chr12 133851895 4669742 0.034887380563420486 0.204195375193733 chr13 115169878 3266324 0.028360922636385878 0.1819323523003358 chr14 107349540 3260038 0.030368439398995094 0.19912471591929112 chr15 102531392 2944190 0.0287150105208754 0.1924154450115566 chr16 90354753 3073591 0.03401692659156514 0.22032029034077552 chr17 81195210 2896821 0.035677240073644735 0.22945766765414613 chr18 78077248 2569142 0.0329051300578627 0.4663429950891593 chr19 59128983 2302479 0.03893993914963834 0.31145221409033014 chr20 63025520 2262656 0.03590063199795892 0.21148217966961347 chr21 48129895 1372526 0.02851712018071097 0.19296884650818458 chr22 51304566 1244538 0.024257840910300265 0.16919709977100106 chrMT 16571 34726 2.0955886790175606 1.7591944423816115 chrX 155270560 5819256 0.037478167142567145 0.2295729327696642 chrY 59373566 266028 0.004480579792023946 0.10149302640658756