BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234063.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,598,178 number of mapped reads = 3,365,796 (93.54%) number of supplementary alignments = 38,583 (1.07%) number of secondary alignments = 0 number of mapped bases = 231,703,917 bp number of sequenced bases = 231,621,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 464,944 duplication rate = 5.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0159 >>>>>>> ACTG content number of A's = 60,283,700 bp (26.03%) number of C's = 41,364,869 bp (17.86%) number of T's = 65,088,983 bp (28.1%) number of G's = 64,834,844 bp (27.99%) number of N's = 48,724 bp (0.02%) GC percentage = 45.85% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,556,774 number of insertions = 15,654 mapped reads with insertion percentage = 0.46% number of deletions = 50,522 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.0748X std coverageData = 36.5247X There is a 4.41% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 18851709 0.07563354877258259 0.8471413309476695 chr2 243199373 39091281 0.1607375895660718 130.294511300005 chr3 198022430 9489103 0.04791933418855632 0.31164076556928366 chr4 191154276 8880772 0.04645866253078221 0.33516212572948917 chr5 180915260 16335281 0.09029244409786107 0.438340593533821 chr6 171115067 6398192 0.03739116672876036 0.29409663809301245 chr7 159138663 12241691 0.07692468171609561 1.0521815679748507 chr8 146364022 12684522 0.08666420768349752 0.8527088167950655 chr9 141213431 8144914 0.05767804055408866 0.5656328437603384 chr10 135534747 8833045 0.0651718116240701 0.56253787479083 chr11 135006516 11402895 0.08446181219875343 0.8647914615732725 chr12 133851895 7662506 0.05724615254793367 0.3510480595948107 chr13 115169878 7796920 0.06769929894342686 0.37390969512172134 chr14 107349540 7983290 0.07436724926813845 0.5274430780977363 chr15 102531392 6867405 0.06697856008821182 0.3735860331283518 chr16 90354753 6124839 0.06778657233449578 0.4454352086217407 chr17 81195210 5778115 0.0711632496547518 0.5030819371793073 chr18 78077248 6103171 0.07816836730720837 1.3668679117719351 chr19 59128983 3211802 0.054318573346678396 0.6426984643928237 chr20 63025520 4880093 0.07743042818210782 0.44787905083453644 chr21 48129895 3315148 0.06887918621056621 0.4044186884799918 chr22 51304566 2791033 0.054401259334305646 0.3369577021422429 chrMT 16571 6968 0.42049363345603763 0.9762739769989616 chrX 155270560 16206301 0.10437458974837213 0.5378096091029025 chrY 59373566 622921 0.010491554440236923 0.19867811967001187