BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818785.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 = 2,014,509 number of mapped reads = 1,963,172 (97.45%) number of supplementary alignments = 12,995 (0.65%) number of secondary alignments = 0 number of mapped bases = 133,431,458 bp number of sequenced bases = 133,378,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 913,698 duplication rate = 38.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7674 >>>>>>> ACTG content number of A's = 36,710,266 bp (27.52%) number of C's = 27,954,670 bp (20.96%) number of T's = 38,514,241 bp (28.88%) number of G's = 30,191,967 bp (22.64%) number of N's = 7,830 bp (0.01%) GC percentage = 43.6% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 643,755 number of insertions = 11,696 mapped reads with insertion percentage = 0.59% number of deletions = 32,805 mapped reads with deletion percentage = 1.66% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.0431X std coverageData = 0.5066X There is a 1.92% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 10969585 0.04401026146289922 0.7261835535321449 chr2 243199373 11779161 0.04843417503383119 0.7255654750825773 chr3 198022430 9106462 0.04598702278322713 0.41139949245549307 chr4 191154276 8846156 0.046277573199565776 0.4426939109014039 chr5 180915260 8297038 0.045861460221763496 0.42639556315824184 chr6 171115067 7834768 0.045786546663363084 0.448013727206432 chr7 159138663 7361653 0.04625936187487009 0.4734942219620876 chr8 146364022 6913544 0.047235269334153715 0.47338100001248845 chr9 141213431 5757191 0.04076942936114908 0.4610391194985193 chr10 135534747 6470300 0.04773904952949077 0.5345676587647324 chr11 135006516 6373174 0.04720641779986382 0.4604463855823691 chr12 133851895 6118440 0.04571052206619861 0.42384576750677333 chr13 115169878 4255039 0.03694576284955342 0.373291825665801 chr14 107349540 4095981 0.038155552413172894 0.40619433870424826 chr15 102531392 3778769 0.03685475176227004 0.3731735349091176 chr16 90354753 4026570 0.044564008713520585 0.518519148706584 chr17 81195210 3574616 0.04402496157100893 0.4310889096351734 chr18 78077248 3587865 0.045952759502998874 0.593577695985439 chr19 59128983 2593032 0.043853823766933385 0.6555854596991973 chr20 63025520 2893043 0.045902723214342384 0.437197522989467 chr21 48129895 1817423 0.03776079295415043 0.39419862608835216 chr22 51304566 1554991 0.03030901771978736 0.35928407614882857 chrMT 16571 61554 3.7145615834892283 4.631561060358246 chrX 155270560 4121580 0.0265445039935452 0.33086612502194773 chrY 59373566 1243523 0.020944051095061395 0.6170161070034952