BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818825.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 = 1,433,037 number of mapped reads = 1,397,329 (97.51%) number of supplementary alignments = 10,814 (0.75%) number of secondary alignments = 0 number of mapped bases = 95,002,189 bp number of sequenced bases = 94,962,905 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 545,035 duplication rate = 33.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6751 >>>>>>> ACTG content number of A's = 26,065,021 bp (27.45%) number of C's = 20,115,477 bp (21.18%) number of T's = 27,201,207 bp (28.64%) number of G's = 21,575,641 bp (22.72%) number of N's = 5,559 bp (0.01%) GC percentage = 43.9% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 468,641 number of insertions = 10,789 mapped reads with insertion percentage = 0.76% number of deletions = 23,610 mapped reads with deletion percentage = 1.67% homopolymer indels = 41.9% >>>>>>> Coverage mean coverageData = 0.0307X std coverageData = 0.3891X There is a 1.65% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.01% 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% 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 7892511 0.031664960224913545 0.5851146796642792 chr2 243199373 8331221 0.034256753614245544 0.5721756032287191 chr3 198022430 6494244 0.032795496954562166 0.3060824581780424 chr4 191154276 6168428 0.032269369689642724 0.3429824073190817 chr5 180915260 5942098 0.03284464782020046 0.31225914484680134 chr6 171115067 5546395 0.03241324739685255 0.3245398343956391 chr7 159138663 5180906 0.03255592262956237 0.35772878509156963 chr8 146364022 4892663 0.033428044222507086 0.3362800501986537 chr9 141213431 4125287 0.029213134832762472 0.33923535561786655 chr10 135534747 4604207 0.03397067616911551 0.40691827330350483 chr11 135006516 4487981 0.033242699189422825 0.332712084540983 chr12 133851895 4378502 0.03271154285861997 0.31734983571701186 chr13 115169878 3019947 0.026221674038762115 0.26787650771493093 chr14 107349540 2917916 0.027181448565126595 0.31287806402646223 chr15 102531392 2767580 0.026992513668399234 0.27518942240173977 chr16 90354753 2840672 0.031439098726770906 0.4142185144268165 chr17 81195210 2635347 0.03245692695418855 0.3225510680032032 chr18 78077248 2451270 0.03139544570013533 0.4075024309148953 chr19 59128983 1991663 0.03368336303027569 0.48997195562119605 chr20 63025520 2077006 0.03295499981594757 0.3194217040252277 chr21 48129895 1296102 0.026929250520908055 0.2893105361026681 chr22 51304566 1177842 0.022957839658949653 0.2711021204208807 chrMT 16571 5577 0.33655180737432866 1.0083248490857353 chrX 155270560 2896120 0.018652087040840197 0.25516110448668833 chrY 59373566 880704 0.01483326772052061 0.5943258312165759