BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081055.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 = 3,001,546 number of mapped reads = 2,740,104 (91.29%) number of supplementary alignments = 28,484 (0.95%) number of secondary alignments = 0 number of mapped bases = 181,571,987 bp number of sequenced bases = 181,503,170 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,735 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.582 >>>>>>> ACTG content number of A's = 49,212,915 bp (27.11%) number of C's = 34,510,316 bp (19.01%) number of T's = 55,401,114 bp (30.52%) number of G's = 42,376,897 bp (23.35%) number of N's = 1,928 bp (0%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,627,250 number of insertions = 15,198 mapped reads with insertion percentage = 0.55% number of deletions = 40,447 mapped reads with deletion percentage = 1.46% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.0587X std coverageData = 0.6042X There is a 4.9% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% 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 15265808 0.061246820323869924 1.0782082816890932 chr2 243199373 12507859 0.0514304738770852 0.6588449652516604 chr3 198022430 15284026 0.07718330696174165 0.3243863275899149 chr4 191154276 10964437 0.057359098783644265 0.3320905022744954 chr5 180915260 9817316 0.05426472040003701 0.277709378764496 chr6 171115067 14731762 0.08609272262389378 0.5913512092099236 chr7 159138663 7004955 0.04401793296453672 0.8541285027181988 chr8 146364022 13658007 0.09331532991078914 0.5662094400161001 chr9 141213431 8989214 0.06365693359578524 0.7592907942726013 chr10 135534747 8399305 0.061971599061604474 0.541465055243564 chr11 135006516 8544478 0.0632893748624696 0.45018179534692787 chr12 133851895 9357633 0.06991035128789173 0.33604975697382217 chr13 115169878 4404858 0.03824661514358815 0.22380773538663049 chr14 107349540 5253661 0.04893976257373809 0.4111482938163665 chr15 102531392 4972948 0.04850171155386245 0.26839672885877097 chr16 90354753 4818845 0.053332501501055514 0.44342678491669757 chr17 81195210 4511376 0.055562095350206 0.2891700264799765 chr18 78077248 4556415 0.05835778177017715 1.4253410935182522 chr19 59128983 4271086 0.07223337495928181 0.7937291624344254 chr20 63025520 3002796 0.047644128917936734 0.2839836347121069 chr21 48129895 3313454 0.06884398979054494 0.4136743596009418 chr22 51304566 1839942 0.03586312376173302 0.21404055854088047 chrMT 16571 311052 18.77086476374389 9.778610558255792 chrX 155270560 5259232 0.03387140485614272 0.29314802002909357 chrY 59373566 531522 0.008952165682620444 0.24116556222929955