BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818859.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 919,061 number of mapped reads = 899,429 (97.86%) number of supplementary alignments = 15,106 (1.64%) number of secondary alignments = 0 number of mapped bases = 83,185,382 bp number of sequenced bases = 83,131,520 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,278 duplication rate = 13.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3327 >>>>>>> ACTG content number of A's = 24,072,169 bp (28.96%) number of C's = 17,708,572 bp (21.3%) number of T's = 23,926,837 bp (28.78%) number of G's = 17,422,745 bp (20.96%) number of N's = 1,197 bp (0%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 515,413 number of insertions = 13,162 mapped reads with insertion percentage = 1.42% number of deletions = 27,464 mapped reads with deletion percentage = 2.98% homopolymer indels = 38.9% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.3415X There is a 2.08% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 7737006 0.031041070104294743 0.4803788327897896 chr2 243199373 6171069 0.02537452676738603 0.5213027321760445 chr3 198022430 5320848 0.026869925795779803 0.20092364192207882 chr4 191154276 4219624 0.02207444211187826 0.23005932213644387 chr5 180915260 3620600 0.020012684391576475 0.18111101833406304 chr6 171115067 4141124 0.024200814531428725 0.2068192985423457 chr7 159138663 7430630 0.04669280148470269 0.645825348876791 chr8 146364022 7346066 0.0501903808027358 0.320368086245333 chr9 141213431 3109400 0.022019151988453563 0.28570347366776194 chr10 135534747 3882591 0.028646462150403396 0.4592152691993533 chr11 135006516 3621500 0.026824631190393803 0.22844511379658922 chr12 133851895 3211587 0.02399358634407081 0.19050026064429706 chr13 115169878 2541310 0.022065752296794132 0.18189011893833737 chr14 107349540 2492557 0.023219074809263274 0.19798933577631608 chr15 102531392 2311869 0.022547913911087836 0.18296638397946577 chr16 90354753 2114415 0.02340125925638909 0.3835147361204877 chr17 81195210 2054774 0.025306591361731808 0.22922139534753574 chr18 78077248 1586088 0.020314343046517212 0.3024504204910945 chr19 59128983 1419989 0.024015109476853338 0.42160491719764653 chr20 63025520 3459440 0.05488951142330916 0.3013550536826507 chr21 48129895 822256 0.017084101263881834 0.18303240894211562 chr22 51304566 754332 0.014703018830721616 0.15744943801929878 chrMT 16571 87586 5.28549876289904 4.069839407239815 chrX 155270560 3397564 0.02188157239852809 0.20433789326593374 chrY 59373566 331157 0.0055775157584437495 0.4096745871224713