BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548954.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,543,467 number of mapped reads = 7,451,571 (87.22%) number of secondary alignments = 0 number of mapped bases = 294,053,283 bp number of sequenced bases = 294,023,149 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 418,053 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 33.8182 >>>>>>> ACTG content number of A's = 82,209,663 bp (27.96%) number of C's = 64,213,935 bp (21.84%) number of T's = 83,792,293 bp (28.5%) number of G's = 63,806,866 bp (21.7%) number of N's = 392 bp (0%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 1,054,851 number of insertions = 11,381 mapped reads with insertion percentage = 0.15% number of deletions = 23,452 mapped reads with deletion percentage = 0.31% homopolymer indels = 38.04% >>>>>>> Coverage mean coverageData = 0.095X std coverageData = 1.1968X There is a 7.65% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 23654743 0.09490344659963756 2.084249312788709 chr2 243199373 24915749 0.10244988995099095 1.1148980763156773 chr3 198022430 19748235 0.09972726321962617 0.3859444211703953 chr4 191154276 19398537 0.10148105188083786 0.44310566539302787 chr5 180915260 18085251 0.09996531525311905 0.41746210000082584 chr6 171115067 17037158 0.09956550465541412 0.4430064386287899 chr7 159138663 17311533 0.10878269726320372 1.8204006226997353 chr8 146364022 15163584 0.10360185373971208 2.7452431904386234 chr9 141213431 12510648 0.08859389585966508 1.167777485144867 chr10 135534747 13964444 0.10303220619875433 0.8747383149024535 chr11 135006516 13430713 0.09948196130029753 0.7552651504745639 chr12 133851895 13639481 0.10189979753368453 0.45403235388147956 chr13 115169878 9180594 0.07971349939261028 0.3250454312167789 chr14 107349540 9016261 0.08398974974648238 0.5606720345788563 chr15 102531392 8249697 0.08046020676282245 0.3500467830462134 chr16 90354753 8409358 0.09307045529746509 0.5475021165473687 chr17 81195210 8160779 0.10050813342314159 0.4234060390566615 chr18 78077248 7842473 0.10044504898533309 2.2641252235113094 chr19 59128983 7077718 0.11969964036080241 2.1568987224962317 chr20 63025520 5914744 0.09384680999061967 0.44201660321503794 chr21 48129895 3720663 0.07730461493838704 0.5664757538227263 chr22 51304566 3388209 0.06604108102191138 0.4656335359538571 chrMT 16571 12883 0.7774425200651741 1.2459762744181933 chrX 155270560 11431563 0.07362350596275302 0.618955613367422 chrY 59373566 2788265 0.046961386823220284 0.4365376379730549