BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714153.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 756,664 number of mapped reads = 654,326 (86.48%) number of supplementary alignments = 19,935 (2.63%) number of secondary alignments = 0 number of mapped bases = 85,344,381 bp number of sequenced bases = 83,414,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 591,464 duplication rate = 43.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4696 >>>>>>> ACTG content number of A's = 22,410,372 bp (26.87%) number of C's = 18,835,948 bp (22.58%) number of T's = 21,217,080 bp (25.44%) number of G's = 20,950,671 bp (25.12%) number of N's = 587 bp (0%) GC percentage = 47.7% >>>>>>> Mismatches and indels general error rate = 0.0441 number of mismatches = 3,451,391 number of insertions = 88,000 mapped reads with insertion percentage = 13% number of deletions = 304,359 mapped reads with deletion percentage = 44.15% homopolymer indels = 29.91% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 7.3543X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7775143 0.031194076744145805 8.229201024073149 chr2 243199373 10123044 0.04162446586570764 11.344534181882961 chr3 198022430 2603703 0.013148525649341845 2.366436571390482 chr4 191154276 2728885 0.014275825040921397 2.95601990074326 chr5 180915260 4589445 0.02536792639824855 4.513610134477697 chr6 171115067 3152392 0.018422644219868726 3.447760962924007 chr7 159138663 2390202 0.015019618456892527 2.4296732852626937 chr8 146364022 3196530 0.02183958842016517 4.712287861726551 chr9 141213431 4312191 0.030536691655059355 8.099007091006685 chr10 135534747 3890052 0.028701510764615953 4.466433202253037 chr11 135006516 3730887 0.027634866157126816 4.726189097769727 chr12 133851895 4766460 0.03560995531665801 9.396157532505839 chr13 115169878 3036838 0.026368335651097936 8.062055366596999 chr14 107349540 4838987 0.045076923478200276 22.381108918188623 chr15 102531392 3363406 0.032803670509028104 6.152813262973279 chr16 90354753 1390968 0.015394519422791185 2.0745831212341392 chr17 81195210 2968100 0.03655511205648707 6.361883605885162 chr18 78077248 2506088 0.03209754524134867 6.959927452807497 chr19 59128983 2065773 0.03493672468542204 3.702972275292847 chr20 63025520 2064145 0.032750939619379575 4.122400880147898 chr21 48129895 848499 0.017629354894707332 3.4702121538624247 chr22 51304566 517049 0.010078030871560242 1.1411194922221208 chrMT 16571 152981 9.2318508237282 77.38036779974144 chrX 155270560 7645268 0.04923836173451039 5.125574231069631 chrY 59373566 687345 0.011576616435671053 2.7909228697415354