BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081054.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 = 2,050,233 number of mapped reads = 1,617,098 (78.87%) number of supplementary alignments = 13,000 (0.63%) number of secondary alignments = 0 number of mapped bases = 106,001,181 bp number of sequenced bases = 105,967,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,476 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5346 >>>>>>> ACTG content number of A's = 30,021,466 bp (28.33%) number of C's = 20,740,015 bp (19.57%) number of T's = 30,724,584 bp (28.99%) number of G's = 24,479,707 bp (23.1%) number of N's = 1,408 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 827,566 number of insertions = 8,241 mapped reads with insertion percentage = 0.5% number of deletions = 19,615 mapped reads with deletion percentage = 1.2% homopolymer indels = 44.06% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.3642X There is a 3.15% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 8562180 0.03435168973962155 0.5853411117959681 chr2 243199373 8908814 0.03663173095433926 0.43728192722903547 chr3 198022430 7033273 0.03551755727873857 0.1973386706731555 chr4 191154276 6649665 0.03478690165424288 0.21218048854301394 chr5 180915260 6281515 0.034720758215752504 0.20045555956708225 chr6 171115067 6139750 0.03588082632138992 0.300706719578933 chr7 159138663 5999380 0.03769907253776538 0.6696845881295183 chr8 146364022 5339534 0.03648119207874733 0.2916632837865852 chr9 141213431 4501751 0.03187905688659318 0.3641154854363916 chr10 135534747 4949473 0.03651811147734684 0.29450296513720753 chr11 135006516 4814300 0.03565976030371749 0.3600652422318786 chr12 133851895 4853166 0.036257730979453076 0.20630944355686545 chr13 115169878 3193840 0.027731556683597426 0.17458968733184257 chr14 107349540 3158888 0.02942619036839841 0.22354506543511235 chr15 102531392 3074844 0.029989293425373566 0.20405733620074473 chr16 90354753 3114998 0.03447519800092863 0.23305085554850913 chr17 81195210 2974667 0.03663599121179685 0.25195007974957245 chr18 78077248 2892642 0.037048462568762666 0.7965519453734703 chr19 59128983 2321398 0.039259900681870345 0.4378163554545311 chr20 63025520 2216665 0.035170911719570104 0.21311338172450928 chr21 48129895 1395456 0.028993539254552704 0.2053765728001095 chr22 51304566 1248595 0.024336917692666965 0.16406062093612067 chrMT 16571 26772 1.6155935067286222 1.6663757297539743 chrX 155270560 6070667 0.03909734723697783 0.2648557844863226 chrY 59373566 278948 0.0046981850475344535 0.10803273262625025