BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082326.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 = 2,228,269 number of mapped reads = 1,996,253 (89.59%) number of supplementary alignments = 18,360 (0.82%) number of secondary alignments = 0 number of mapped bases = 134,230,102 bp number of sequenced bases = 134,183,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,270 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3379 >>>>>>> ACTG content number of A's = 37,774,675 bp (28.15%) number of C's = 24,934,588 bp (18.58%) number of T's = 41,941,736 bp (31.26%) number of G's = 29,529,679 bp (22.01%) number of N's = 2,732 bp (0%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,104,345 number of insertions = 10,517 mapped reads with insertion percentage = 0.52% number of deletions = 29,062 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.87% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.3298X There is a 3.83% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.05% 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 10457342 0.04195512917097206 0.4845143329771172 chr2 243199373 11445132 0.047060696986254154 0.44688340381657615 chr3 198022430 9134138 0.046126784728376474 0.23645834338438285 chr4 191154276 9107964 0.04764718943561587 0.24461352882195997 chr5 180915260 8978801 0.049629870913045146 0.24551539863261124 chr6 171115067 7622650 0.04454692467262395 0.26508142381745103 chr7 159138663 7186228 0.04515702133302452 0.3503018263298452 chr8 146364022 7004094 0.04785393230038459 0.5909335397850365 chr9 141213431 5733518 0.040601789499753745 0.30160493048442494 chr10 135534747 6277357 0.04631548100355402 0.28488485165446453 chr11 135006516 6186985 0.04582730658718724 0.29020484457839146 chr12 133851895 5872162 0.04387059294154932 0.23275400046569375 chr13 115169878 4494485 0.03902483078084011 0.21873757220502657 chr14 107349540 4152429 0.038681386059036676 0.22499594939968912 chr15 102531392 3931608 0.038345407424098955 0.21908495956350427 chr16 90354753 3450422 0.038187498559151614 0.22919310047075359 chr17 81195210 3349604 0.04125371435088351 0.23365691122672444 chr18 78077248 3709809 0.047514597338266844 0.4885175570369083 chr19 59128983 2419835 0.0409246849383491 0.37911797802964997 chr20 63025520 2751208 0.04365228561382754 0.23421209882619776 chr21 48129895 1724065 0.03582108375677944 0.2163028779683949 chr22 51304566 1384846 0.026992646229577304 0.17999665091926453 chrMT 16571 37269 2.2490495443847687 1.8490116752528072 chrX 155270560 7523286 0.04845275240844111 0.26123355792365677 chrY 59373566 294865 0.004966267311618103 0.10068350771627449