BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082903.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 = 3,274,630 number of mapped reads = 2,817,872 (86.05%) number of supplementary alignments = 14,466 (0.44%) number of secondary alignments = 0 number of mapped bases = 187,917,132 bp number of sequenced bases = 187,847,372 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,786 duplication rate = 3.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5912 >>>>>>> ACTG content number of A's = 52,086,146 bp (27.73%) number of C's = 32,707,506 bp (17.41%) number of T's = 62,316,561 bp (33.17%) number of G's = 40,688,555 bp (21.66%) number of N's = 48,604 bp (0.03%) GC percentage = 39.07% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,754,157 number of insertions = 16,235 mapped reads with insertion percentage = 0.57% number of deletions = 43,164 mapped reads with deletion percentage = 1.52% homopolymer indels = 49.45% >>>>>>> Coverage mean coverageData = 0.0607X std coverageData = 0.3774X There is a 4.82% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 14750428 0.05917910230602796 0.5290800183797656 chr2 243199373 16819455 0.06915912155743921 0.43375786385350795 chr3 198022430 14173700 0.07157623507599618 0.3231954850267993 chr4 191154276 13349696 0.06983728682062022 0.3293858980081989 chr5 180915260 10606532 0.05862707214416296 0.292757234307188 chr6 171115067 11027744 0.06444636462083143 0.43228201577326186 chr7 159138663 10102523 0.06348251775874227 0.42027590506840534 chr8 146364022 9698784 0.06626480925756467 0.5004928591607131 chr9 141213431 7894475 0.05590456193929599 0.3823642689177487 chr10 135534747 9353935 0.06901503272810182 0.33820709763895407 chr11 135006516 8480881 0.06281830871037365 0.3407227114983312 chr12 133851895 7779916 0.05812331607258903 0.29690702897151844 chr13 115169878 6350826 0.055143116501347685 0.2856957642925042 chr14 107349540 5784730 0.05388686341832485 0.3027270479120307 chr15 102531392 5588940 0.05450954962164173 0.28243254309169974 chr16 90354753 4718907 0.05222643904521548 0.29853050933548875 chr17 81195210 4233229 0.052136437605124736 0.29288879212605035 chr18 78077248 5433191 0.06958737838710709 0.5816363208297127 chr19 59128983 2838941 0.0480126810231118 0.37729952970402864 chr20 63025520 3749973 0.05949927902221196 0.30608566866035786 chr21 48129895 2346008 0.0487432602959138 0.28316012012954184 chr22 51304566 1695800 0.03305358825177471 0.21760227068899796 chrMT 16571 21852 1.3186892764468046 1.4418890228747225 chrX 155270560 10734150 0.06913190755543099 0.3321479435506359 chrY 59373566 382516 0.00644253033412209 0.13541610185356506