BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472811.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,622,902 number of mapped reads = 2,188,324 (83.43%) number of supplementary alignments = 20,716 (0.79%) number of secondary alignments = 0 number of mapped bases = 139,556,048 bp number of sequenced bases = 139,497,808 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,424 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5267 >>>>>>> ACTG content number of A's = 37,458,703 bp (26.85%) number of C's = 28,037,447 bp (20.1%) number of T's = 41,110,560 bp (29.47%) number of G's = 32,888,519 bp (23.58%) number of N's = 2,579 bp (0%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,210,670 number of insertions = 10,963 mapped reads with insertion percentage = 0.5% number of deletions = 32,142 mapped reads with deletion percentage = 1.45% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.3392X There is a 3.84% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.09% 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% 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 11497906 0.0461298991106626 0.3999155327176101 chr2 243199373 12073271 0.04964351203323209 0.48323806087095106 chr3 198022430 10506005 0.0530546211355956 0.264165939751861 chr4 191154276 6430595 0.03364086398988009 0.23937388803525564 chr5 180915260 8167508 0.045145489661845 0.24472420655694418 chr6 171115067 9599538 0.056099899139799306 0.29617767167739373 chr7 159138663 7639554 0.04800564398357425 0.4294745346633995 chr8 146364022 7188538 0.049114105377618004 0.3327685516104934 chr9 141213431 5969262 0.042271205775037075 0.375594443174026 chr10 135534747 6537168 0.04823241378832544 0.328510948006169 chr11 135006516 5280060 0.0391096678622534 0.3539846257902965 chr12 133851895 6571396 0.04909453093659974 0.2627853545304123 chr13 115169878 6399251 0.055563582345724116 0.27730212058201675 chr14 107349540 3323724 0.030961697646771473 0.2358720713055444 chr15 102531392 3112234 0.0303539622284656 0.22094926599821585 chr16 90354753 4252150 0.04706061229562544 0.2810066357038657 chr17 81195210 3606927 0.04442290376488958 0.26390834202352575 chr18 78077248 2996182 0.03837458512882012 0.6832631435477877 chr19 59128983 3251432 0.05498880303758987 0.3397506943568584 chr20 63025520 4632404 0.0735004487071269 0.3342701587411115 chr21 48129895 1922002 0.03993364207422435 0.2691519981862598 chr22 51304566 1911965 0.03726695592747047 0.23399454969684894 chrMT 16571 73141 4.413795184358216 3.798981758678911 chrX 155270560 5902776 0.03801606692215189 0.26468638127643335 chrY 59373566 711059 0.011976019766102646 0.16746242302497974