BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708516.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,377,568 number of mapped reads = 2,225,177 (65.88%) number of supplementary alignments = 959 (0.03%) number of secondary alignments = 0 number of mapped bases = 105,370,505 bp number of sequenced bases = 105,344,676 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,265 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2396 >>>>>>> ACTG content number of A's = 29,706,209 bp (28.2%) number of C's = 19,733,620 bp (18.73%) number of T's = 33,472,030 bp (31.77%) number of G's = 22,431,356 bp (21.29%) number of N's = 1,461 bp (0%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 556,749 number of insertions = 6,223 mapped reads with insertion percentage = 0.28% number of deletions = 17,017 mapped reads with deletion percentage = 0.76% homopolymer indels = 46.88% >>>>>>> Coverage mean coverageData = 0.034X std coverageData = 0.3262X There is a 2.96% of reference with a coverageData >= 1X There is a 0.32% 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 0.01% 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 8761960 0.03515321231636972 0.46722290529714017 chr2 243199373 9207782 0.03786104333418656 0.529404073560075 chr3 198022430 7196410 0.03634138819526657 0.22865572029018302 chr4 191154276 7021045 0.036729730283407314 0.23028870566275056 chr5 180915260 6420402 0.03548844912253394 0.2181831118901762 chr6 171115067 6345585 0.037083730329837056 0.34321089272087135 chr7 159138663 5954531 0.03741724913197241 0.4084709298507436 chr8 146364022 5428554 0.037089401656371535 0.46304585902790535 chr9 141213431 4446075 0.031484788440555626 0.2630197815848662 chr10 135534747 5004194 0.03692185296217803 0.26899697404640766 chr11 135006516 4895476 0.036261034985896536 0.28862438162783344 chr12 133851895 5033495 0.0376049588240794 0.23204016197359675 chr13 115169878 3441243 0.029879713860598168 0.2804642890120801 chr14 107349540 3339358 0.03110733404167358 0.21312445379266615 chr15 102531392 3069774 0.029939845154935574 0.2123251754750632 chr16 90354753 2890598 0.03199165405277573 0.21683817839219008 chr17 81195210 3018314 0.037173547552866726 0.2537112214093475 chr18 78077248 2734139 0.03501838333236335 0.3600347091964892 chr19 59128983 2122738 0.035900127015544986 0.35693273433518624 chr20 63025520 2095725 0.03325200648880009 0.2179427507856071 chr21 48129895 1204852 0.025033339466042883 0.20197227891146183 chr22 51304566 1232711 0.02402731561943239 0.19316838429958955 chrMT 16571 115040 6.94224850642689 4.692273022974386 chrX 155270560 3648088 0.02349503988392906 0.2048689103928697 chrY 59373566 742416 0.012504150416028575 0.1456027730585581