BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818776.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 = 556,665 number of mapped reads = 541,878 (97.34%) number of supplementary alignments = 4,654 (0.84%) number of secondary alignments = 0 number of mapped bases = 36,777,462 bp number of sequenced bases = 36,763,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,072 duplication rate = 24.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9541 >>>>>>> ACTG content number of A's = 10,735,163 bp (29.2%) number of C's = 7,827,988 bp (21.29%) number of T's = 10,318,495 bp (28.07%) number of G's = 7,879,355 bp (21.43%) number of N's = 2,027 bp (0.01%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 183,483 number of insertions = 3,822 mapped reads with insertion percentage = 0.7% number of deletions = 9,197 mapped reads with deletion percentage = 1.68% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 0.0119X std coverageData = 0.1836X There is a 0.77% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 3014840 0.012095616804902565 0.2388059385331121 chr2 243199373 3300779 0.013572317063498351 0.24812603391962443 chr3 198022430 2541531 0.01283456121612082 0.16656612668922416 chr4 191154276 2478123 0.012963994590421822 0.17224998861020874 chr5 180915260 2305063 0.012741119792769278 0.16513147794014488 chr6 171115067 2164285 0.012648126421269496 0.16947683602694477 chr7 159138663 1981809 0.012453347053694927 0.17701284203891243 chr8 146364022 1937108 0.013234864507891153 0.1779480375036385 chr9 141213431 1601406 0.011340323570213374 0.17135935775626399 chr10 135534747 1735668 0.012806074002558178 0.18977582103435228 chr11 135006516 1756001 0.01300678702056129 0.175176978525479 chr12 133851895 1666199 0.012448079274484684 0.1673179418879977 chr13 115169878 1209943 0.010505724422144478 0.15156860295861652 chr14 107349540 1156890 0.01077685102330201 0.15752694055785202 chr15 102531392 1050809 0.01024865633346712 0.1454057423722294 chr16 90354753 1062842 0.011762989380315168 0.195438319317397 chr17 81195210 945930 0.01165007147589125 0.16226246957207524 chr18 78077248 1035705 0.013265131988258603 0.2053566261716006 chr19 59128983 684105 0.011569706855942373 0.199483360139449 chr20 63025520 742491 0.011780799269883057 0.1647357540659878 chr21 48129895 478199 0.009935592005758583 0.14894370296334894 chr22 51304566 400000 0.007796577014217409 0.13496303737377566 chrMT 16571 31783 1.9179892583428881 2.5327564163301006 chrX 155270560 1150276 0.00740820410514395 0.13142589867728874 chrY 59373566 345677 0.005822069033212524 0.19668260033478582