BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818926.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,313,357 number of mapped reads = 1,297,589 (98.8%) number of supplementary alignments = 18,713 (1.42%) number of secondary alignments = 0 number of mapped bases = 120,291,702 bp number of sequenced bases = 120,228,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 485,062 duplication rate = 31.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1772 >>>>>>> ACTG content number of A's = 34,268,284 bp (28.5%) number of C's = 24,681,026 bp (20.53%) number of T's = 34,654,403 bp (28.82%) number of G's = 26,619,468 bp (22.14%) number of N's = 5,268 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 722,791 number of insertions = 13,649 mapped reads with insertion percentage = 1.03% number of deletions = 36,149 mapped reads with deletion percentage = 2.73% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 0.0389X std coverageData = 0.4475X There is a 2.1% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 14193949 0.056946494026989807 0.7530029302108927 chr2 243199373 10564720 0.04344057252154182 0.614763378139061 chr3 198022430 8418332 0.042512012401827406 0.3480152540405656 chr4 191154276 7837861 0.0410028023647245 0.3514657458186287 chr5 180915260 6421531 0.035494689613247664 0.32247081952910944 chr6 171115067 6628213 0.03873541422275807 0.3508080913797551 chr7 159138663 6000446 0.037705771098504204 0.37297292795182657 chr8 146364022 7667900 0.052389240847726906 0.42081945895423367 chr9 141213431 4675484 0.03310934354395794 0.49808441745101795 chr10 135534747 5858663 0.043226280564053435 0.4889753989839927 chr11 135006516 4553777 0.03373005344423524 0.3375795504622736 chr12 133851895 5533012 0.04133682231394632 0.3519694015979836 chr13 115169878 1988594 0.01726661549472163 0.21570941357600804 chr14 107349540 2657651 0.0247569854514514 0.2874348908123849 chr15 102531392 3564066 0.03476072966999219 0.31307355223362354 chr16 90354753 3268671 0.03617597183847097 0.4474851502769982 chr17 81195210 2526283 0.031113695007377897 0.3165728516471428 chr18 78077248 3104531 0.0397623005360025 0.6028083768793729 chr19 59128983 1843961 0.03118540022919048 0.6063033942901451 chr20 63025520 2515458 0.03991173734068358 0.3520853710616273 chr21 48129895 1550252 0.03220975237947226 0.3236823608144927 chr22 51304566 1535034 0.029920027001105517 0.31439906604943807 chrMT 16571 5533 0.3338965662905075 1.2960147503873438 chrX 155270560 7052168 0.04541857773939889 0.41230287197866095 chrY 59373566 325612 0.005484124029201817 0.3342039398682364