BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238082.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 = 3,880,733 number of mapped reads = 3,356,609 (86.49%) number of supplementary alignments = 34,850 (0.9%) number of secondary alignments = 0 number of mapped bases = 236,916,802 bp number of sequenced bases = 236,785,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 267,649 duplication rate = 6.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8641 >>>>>>> ACTG content number of A's = 69,225,077 bp (29.24%) number of C's = 46,364,270 bp (19.58%) number of T's = 72,240,526 bp (30.51%) number of G's = 48,940,614 bp (20.67%) number of N's = 15,298 bp (0.01%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,804,587 number of insertions = 21,079 mapped reads with insertion percentage = 0.62% number of deletions = 77,960 mapped reads with deletion percentage = 2.29% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.0765X std coverageData = 0.8366X There is a 3.34% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 18616022 0.07468796637421417 1.562071716715471 chr2 243199373 19633393 0.08072962013763087 0.8524413278610851 chr3 198022430 16053907 0.08107115441417419 0.5689622698255945 chr4 191154276 15805456 0.08268429213689156 0.6035483814020934 chr5 180915260 16289788 0.0900409838285615 0.5966420571403459 chr6 171115067 14737561 0.08612661210014896 0.7038886759139396 chr7 159138663 12075733 0.07588183017473259 1.171879197898663 chr8 146364022 13025030 0.08899065372773099 0.8265262193311815 chr9 141213431 10500488 0.07435898926639634 0.7620501902264554 chr10 135534747 12538210 0.09250919249511713 1.0351625441942416 chr11 135006516 11427334 0.08464283309110798 0.7141520380475125 chr12 133851895 12843584 0.09595369568731171 0.6282345025868964 chr13 115169878 6855540 0.059525460294400936 0.47704645978121635 chr14 107349540 6739792 0.06278361323206415 0.5122419005051895 chr15 102531392 5577611 0.05439905663233364 0.4549256171167784 chr16 90354753 6171175 0.06829939538432472 0.5751031387892789 chr17 81195210 5970109 0.07352784727079344 0.59819671766198 chr18 78077248 5332338 0.06829567046215564 1.3158688238001188 chr19 59128983 3866615 0.06539288862790013 1.0136576251218385 chr20 63025520 4721593 0.07491557388181803 0.5542580656390761 chr21 48129895 3317025 0.06891818484125095 0.5578620643726313 chr22 51304566 2220882 0.04328819388122297 0.39659612321592125 chrMT 16571 85333 5.1495383501297445 5.1205815517904885 chrX 155270560 11820532 0.07612861060074749 0.5724259160898655 chrY 59373566 691751 0.011650824543703506 0.3217632909706657