BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548930.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,693,357 number of mapped reads = 5,822,667 (86.99%) number of secondary alignments = 0 number of mapped bases = 230,656,982 bp number of sequenced bases = 230,634,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,007 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6082 >>>>>>> ACTG content number of A's = 67,696,128 bp (29.35%) number of C's = 47,638,486 bp (20.66%) number of T's = 67,884,046 bp (29.43%) number of G's = 47,413,489 bp (20.56%) number of N's = 2,097 bp (0%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 631,612 number of insertions = 7,293 mapped reads with insertion percentage = 0.13% number of deletions = 17,252 mapped reads with deletion percentage = 0.3% homopolymer indels = 40.95% >>>>>>> Coverage mean coverageData = 0.0745X std coverageData = 0.9072X There is a 6.35% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 18065640 0.07247981941838372 0.9182596247892195 chr2 243199373 19473523 0.08007225824550132 0.4768444983611266 chr3 198022430 15708519 0.07932696816214203 0.3196742607647422 chr4 191154276 15433173 0.08073673957468783 0.33360909407457845 chr5 180915260 14474999 0.08000982891106034 0.3289983019121954 chr6 171115067 13446865 0.07858375791069293 0.3548011577775697 chr7 159138663 12868815 0.08086542112019629 0.6839048926409419 chr8 146364022 12191269 0.08329416501003231 3.535268451716766 chr9 141213431 9698866 0.06868231960173816 0.45309333926449646 chr10 135534747 10653338 0.07860226425921613 0.4374751618381777 chr11 135006516 10465071 0.07751530303915109 0.5350579896683921 chr12 133851895 10491424 0.07838084025631464 0.33003074948936234 chr13 115169878 7552870 0.06558025528168052 0.286655705285039 chr14 107349540 7147630 0.06658277250186634 0.3469136163707158 chr15 102531392 6610926 0.06447709205001333 0.2862824628854696 chr16 90354753 6237585 0.06903438715614661 0.33395325228878964 chr17 81195210 5815665 0.07162571535931737 0.3316701780184177 chr18 78077248 6101198 0.07814309746163184 0.8485413700591272 chr19 59128983 4387030 0.07419424074992123 0.8101728574161123 chr20 63025520 4556272 0.07229249358037823 0.3169110495162777 chr21 48129895 2906648 0.060391737817005416 0.32008717746022475 chr22 51304566 2461553 0.047979218847694766 0.26286919499805017 chrMT 16571 9741 0.5878341681250377 0.9208978256572435 chrX 155270560 13195104 0.08498136414269389 0.41111286962442967 chrY 59373566 703258 0.011844631329706557 0.16863053571845657