BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081007.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 = 3,138,339 number of mapped reads = 2,518,882 (80.26%) number of supplementary alignments = 10,426 (0.33%) number of secondary alignments = 0 number of mapped bases = 158,738,145 bp number of sequenced bases = 158,680,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,534 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5311 >>>>>>> ACTG content number of A's = 44,393,444 bp (27.98%) number of C's = 32,286,479 bp (20.35%) number of T's = 45,824,591 bp (28.88%) number of G's = 36,173,644 bp (22.8%) number of N's = 2,023 bp (0%) GC percentage = 43.14% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,182,046 number of insertions = 10,996 mapped reads with insertion percentage = 0.43% number of deletions = 33,088 mapped reads with deletion percentage = 1.3% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0.0513X std coverageData = 0.3974X There is a 4.37% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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% 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 13080679 0.05248002571676642 0.6198476038336231 chr2 243199373 12810367 0.05267434221551221 0.472628598233437 chr3 198022430 10444008 0.052741540440646044 0.259723464546167 chr4 191154276 10013751 0.05238570232140661 0.2794305717667571 chr5 180915260 9641644 0.053293702255962264 0.2773718447964648 chr6 171115067 9341061 0.05458935419170306 0.38183732592096864 chr7 159138663 8716507 0.05477303149141073 0.647770274282854 chr8 146364022 8112993 0.05543024090988699 0.3749625017533184 chr9 141213431 6253302 0.044282629178523394 0.36967578410826174 chr10 135534747 7512244 0.05542670175936507 0.35876848545646717 chr11 135006516 7288626 0.053987216439242085 0.38465688413538146 chr12 133851895 7062421 0.052762951170769755 0.2641152452036052 chr13 115169878 5033833 0.04370789556623478 0.2391496380269001 chr14 107349540 4862030 0.045291577402194735 0.26422871717796415 chr15 102531392 4504354 0.04393146247346374 0.254809088406609 chr16 90354753 4802750 0.05315437030744802 0.2969912853837464 chr17 81195210 4415784 0.05438478452115587 0.31213233147737457 chr18 78077248 4253222 0.05447453783207113 0.712644745008729 chr19 59128983 3490972 0.05903994661974822 0.4738964704376769 chr20 63025520 3561861 0.05651458329895572 0.29538409496634815 chr21 48129895 2000671 0.041568156340253806 0.2558111364551002 chr22 51304566 1937502 0.03776470889550065 0.22111198252294215 chrMT 16571 34965 2.110011465813771 2.0105828449365495 chrX 155270560 9148485 0.05891963679399366 0.3184155832489704 chrY 59373566 414113 0.006974703186936759 0.15292917095054856