BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085019.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,190,204 number of mapped reads = 1,862,490 (85.04%) number of supplementary alignments = 14,907 (0.68%) number of secondary alignments = 0 number of mapped bases = 120,449,065 bp number of sequenced bases = 120,403,707 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,863 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0732 >>>>>>> ACTG content number of A's = 33,149,194 bp (27.53%) number of C's = 23,330,606 bp (19.38%) number of T's = 36,314,325 bp (30.16%) number of G's = 27,597,216 bp (22.92%) number of N's = 12,366 bp (0.01%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,069,954 number of insertions = 8,649 mapped reads with insertion percentage = 0.46% number of deletions = 25,662 mapped reads with deletion percentage = 1.36% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.0389X std coverageData = 0.2887X There is a 3.37% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10698778 0.042923776707461045 0.35438875876154646 chr2 243199373 11733686 0.04824718853201978 0.38157150219218183 chr3 198022430 7780393 0.039290463206617554 0.2241915063057554 chr4 191154276 6613474 0.03459757290493465 0.21248715936985627 chr5 180915260 5932759 0.03279302696743216 0.2034375047125869 chr6 171115067 7909480 0.04622316514068279 0.27866947037928674 chr7 159138663 10515191 0.06607565252700408 0.3870902838929525 chr8 146364022 7332784 0.05009963445798176 0.4788172706907955 chr9 141213431 3911577 0.0276997518741684 0.24965915582099213 chr10 135534747 9099066 0.06713456291765535 0.39726858976632345 chr11 135006516 4471949 0.033123949365525436 0.26197989033855124 chr12 133851895 5261124 0.039305562315722166 0.2271028604802232 chr13 115169878 2199508 0.019097945037329988 0.15340488482832565 chr14 107349540 4112586 0.03831023402615419 0.22943029653109767 chr15 102531392 2228526 0.021735060419349424 0.18753225284219277 chr16 90354753 3219363 0.035630256219061324 0.2179115197892901 chr17 81195210 2143894 0.026404193055230722 0.19175199138009805 chr18 78077248 2656635 0.03402572539441964 0.3370255582641654 chr19 59128983 2191381 0.03706102978297462 0.2995315959503589 chr20 63025520 2800006 0.04442654340654389 0.23945682585092506 chr21 48129895 1318295 0.027390356866558715 0.1892155454009134 chr22 51304566 893651 0.017418547113331004 0.14697830684155258 chrMT 16571 5455 0.3291895480055519 0.693046361396335 chrX 155270560 5174450 0.03332537732845171 0.21893466724712415 chrY 59373566 245054 0.004127324944572135 0.08511965286486152