BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080953.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 = 4,543,359 number of mapped reads = 4,130,080 (90.9%) number of supplementary alignments = 53,667 (1.18%) number of secondary alignments = 0 number of mapped bases = 285,809,877 bp number of sequenced bases = 285,700,745 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 224,728 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9273 >>>>>>> ACTG content number of A's = 82,804,906 bp (28.98%) number of C's = 51,595,098 bp (18.06%) number of T's = 90,267,630 bp (31.6%) number of G's = 59,642,551 bp (20.88%) number of N's = 1,390,560 bp (0.49%) GC percentage = 38.94% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 3,342,999 number of insertions = 22,955 mapped reads with insertion percentage = 0.55% number of deletions = 65,717 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.94% >>>>>>> Coverage mean coverageData = 0.0923X std coverageData = 0.8471X There is a 6.46% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 24534223 0.09843194332502786 1.2851043281133498 chr2 243199373 19992271 0.08220527361310262 0.7350808897627586 chr3 198022430 26054105 0.13157148409904879 0.4852286914940543 chr4 191154276 15412867 0.08063051124213408 0.4359630552978224 chr5 180915260 12299993 0.0679875926442026 0.3580385438567636 chr6 171115067 24307858 0.14205562622957102 0.8813670218065046 chr7 159138663 15104194 0.09491215846145445 0.8436664889190625 chr8 146364022 20095042 0.13729495627005933 1.9970738163004624 chr9 141213431 15138091 0.10720007928990834 0.9577831840263307 chr10 135534747 13250695 0.09776603633605484 0.6859572771817545 chr11 135006516 13553862 0.10039413208766901 0.6463341008133111 chr12 133851895 14766333 0.11031844562230517 0.47914195424839945 chr13 115169878 7771674 0.06748009232066739 0.3434349796452069 chr14 107349540 8494287 0.07912737213405852 0.53816795265058 chr15 102531392 7236387 0.07057728232149622 0.35027439966737217 chr16 90354753 6771481 0.07494327387514413 0.5173361913021428 chr17 81195210 5921336 0.07292715912675145 0.40375822790783905 chr18 78077248 7393670 0.09469685714332554 1.8178381904215 chr19 59128983 5538570 0.09366929243481154 0.9162592511895099 chr20 63025520 4592137 0.07286154878214413 0.40534072006546706 chr21 48129895 5538107 0.11506584421179394 0.5913766080836631 chr22 51304566 2294969 0.04473225638435378 0.27197262353257107 chrMT 16571 58915 3.555307464848229 3.0789421152038225 chrX 155270560 8977165 0.05781627244726882 0.3759521713050088 chrY 59373566 711645 0.011985889478155987 0.2668836803544887