BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234057.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 = 4,497,640 number of mapped reads = 4,180,777 (92.95%) number of supplementary alignments = 21,968 (0.49%) number of secondary alignments = 0 number of mapped bases = 261,482,317 bp number of sequenced bases = 261,358,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 397,024 duplication rate = 7.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0565 >>>>>>> ACTG content number of A's = 64,363,235 bp (24.63%) number of C's = 47,232,861 bp (18.07%) number of T's = 85,060,852 bp (32.55%) number of G's = 64,678,108 bp (24.75%) number of N's = 23,337 bp (0.01%) GC percentage = 42.82% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,730,072 number of insertions = 20,722 mapped reads with insertion percentage = 0.49% number of deletions = 73,474 mapped reads with deletion percentage = 1.74% homopolymer indels = 43.23% >>>>>>> Coverage mean coverageData = 0.0845X std coverageData = 0.9094X There is a 6.6% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% 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% 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 18363969 0.07367672315648914 1.5459116271620739 chr2 243199373 17119519 0.07039294052785243 1.7162688446304983 chr3 198022430 27442875 0.1385846795234257 0.4718004636975682 chr4 191154276 10939121 0.05722666125449373 0.3633160394853296 chr5 180915260 14898238 0.08234926119554536 0.36716401243207464 chr6 171115067 20053035 0.1171903523843403 0.8534246366416526 chr7 159138663 16730226 0.10512986401048248 1.4600999414286033 chr8 146364022 15884020 0.10852407431110359 0.7141230450140801 chr9 141213431 11341168 0.08031224735273233 0.6208674166055326 chr10 135534747 11757804 0.0867512151699372 0.7607948731244399 chr11 135006516 10612047 0.07860396160434212 0.578708120681498 chr12 133851895 8160533 0.06096688433137237 0.3277741629108687 chr13 115169878 12917141 0.11215728647381219 0.4910339095382575 chr14 107349540 7869608 0.07330826010060221 0.4381346357856343 chr15 102531392 4680231 0.04564681029591405 0.3549419073316367 chr16 90354753 8738479 0.09671299748890907 0.48684405415380244 chr17 81195210 6662238 0.08205210627572734 0.42413966414846294 chr18 78077248 5350947 0.06853401134220305 1.5882921106972623 chr19 59128983 7860881 0.13294463393696454 1.0465307107641606 chr20 63025520 5884356 0.09336465609486443 0.4428413913983148 chr21 48129895 4800186 0.09973398030475654 0.4340104587260494 chr22 51304566 2071521 0.040376932532671654 0.24469726400481026 chrMT 16571 142366 8.591273912256352 8.682017830988263 chrX 155270560 10492982 0.06757869618039633 0.43983500428702393 chrY 59373566 708826 0.011938410436725326 0.2978244030337664