BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080993.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 = 3,481,960 number of mapped reads = 3,010,900 (86.47%) number of supplementary alignments = 16,469 (0.47%) number of secondary alignments = 0 number of mapped bases = 195,707,411 bp number of sequenced bases = 195,639,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,213 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8358 >>>>>>> ACTG content number of A's = 54,358,396 bp (27.78%) number of C's = 39,384,338 bp (20.13%) number of T's = 57,621,402 bp (29.45%) number of G's = 44,273,303 bp (22.63%) number of N's = 2,547 bp (0%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,504,188 number of insertions = 13,912 mapped reads with insertion percentage = 0.46% number of deletions = 38,274 mapped reads with deletion percentage = 1.26% homopolymer indels = 45.82% >>>>>>> Coverage mean coverageData = 0.0632X std coverageData = 0.5354X There is a 5.31% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14993928 0.060156030664413065 0.9202094651853647 chr2 243199373 16648475 0.06845607698174452 0.5833458299077394 chr3 198022430 13368324 0.06750914025244514 0.32672607290455086 chr4 191154276 12486837 0.06532334646806436 0.3280340123075062 chr5 180915260 12321655 0.06810732825965041 0.30346467132314797 chr6 171115067 11895356 0.06951670714069849 0.4722250621014684 chr7 159138663 11317052 0.07111440919922772 0.9913045506168136 chr8 146364022 10372408 0.07086719713127315 0.49932335375939385 chr9 141213431 7601048 0.05382666468885668 0.48310327019520644 chr10 135534747 9013156 0.06650070332148847 0.46951303774189984 chr11 135006516 8693936 0.06439641772549705 0.48436208054560576 chr12 133851895 8170786 0.061043483919297516 0.29146782609031985 chr13 115169878 6357953 0.05520499900156185 0.2677628973433509 chr14 107349540 5995086 0.055846406048875474 0.31565648399553475 chr15 102531392 5547275 0.05410318627099103 0.2869159553649953 chr16 90354753 5690104 0.06297514863440554 0.33766581553194014 chr17 81195210 4962446 0.06111747232379841 0.34498745684678983 chr18 78077248 5306976 0.06797083831643247 1.022772114283234 chr19 59128983 4004668 0.06772766580477124 0.6939857537689015 chr20 63025520 4049285 0.06424833940283238 0.3076482264987304 chr21 48129895 2535602 0.05268247520589854 0.30412297227064666 chr22 51304566 2219128 0.04325400589101563 0.2363524314995762 chrMT 16571 64325 3.881781425381691 2.823128878652324 chrX 155270560 11568554 0.07450577881602281 0.4000814526137561 chrY 59373566 523048 0.008809442235623846 0.1888093154059902