BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081912.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 = 2,918,975 number of mapped reads = 2,715,797 (93.04%) number of supplementary alignments = 20,500 (0.7%) number of secondary alignments = 0 number of mapped bases = 185,916,586 bp number of sequenced bases = 185,848,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,963 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8064 >>>>>>> ACTG content number of A's = 52,753,398 bp (28.39%) number of C's = 34,713,253 bp (18.68%) number of T's = 58,293,813 bp (31.37%) number of G's = 40,085,481 bp (21.57%) number of N's = 2,270 bp (0%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,571,089 number of insertions = 14,721 mapped reads with insertion percentage = 0.54% number of deletions = 41,433 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.0601X std coverageData = 0.4462X There is a 5.06% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% 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 14754277 0.05919454459453483 0.7330465967089953 chr2 243199373 15771434 0.06484981357250456 0.5342738727542623 chr3 198022430 12766691 0.06447093392400043 0.2915969423927626 chr4 191154276 12519320 0.06549327727306503 0.31758087043996797 chr5 180915260 11629452 0.06428121099347839 0.29032356399678405 chr6 171115067 11157567 0.06520505292500046 0.3435422617892872 chr7 159138663 10216169 0.06419664968531248 0.5399387480405006 chr8 146364022 9674526 0.06609907180604807 0.6904369342856082 chr9 141213431 7644709 0.05413584916012699 0.432771534953491 chr10 135534747 8663993 0.06392451523888557 0.46895812384906543 chr11 135006516 8477175 0.06279085818346723 0.38647147632824497 chr12 133851895 8440336 0.06305727685065647 0.2907970721640818 chr13 115169878 6232512 0.05411581663740236 0.264507645658002 chr14 107349540 5657327 0.052700058146499744 0.28171720500613445 chr15 102531392 5094791 0.049690059801392336 0.2646280618384011 chr16 90354753 5010992 0.05545908581035023 0.30914736363315637 chr17 81195210 4592604 0.056562499191762663 0.29976003816352725 chr18 78077248 4880147 0.06250408569728277 0.7641186699297157 chr19 59128983 3201960 0.05415212367173641 0.5790385284477619 chr20 63025520 3630070 0.05759682744386718 0.28500591816789167 chr21 48129895 2369449 0.04923029647166278 0.2807486298379989 chr22 51304566 1814039 0.03535823692573484 0.211073136987008 chrMT 16571 86768 5.236135417295275 3.5717405514232023 chrX 155270560 11149730 0.07180839690408794 0.3427093414985862 chrY 59373566 480548 0.008093635474076124 0.17898319718767586