BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472833.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 3,453,604 number of mapped reads = 2,810,648 (81.38%) number of supplementary alignments = 17,889 (0.52%) number of secondary alignments = 0 number of mapped bases = 183,972,944 bp number of sequenced bases = 183,897,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,737 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8357 >>>>>>> ACTG content number of A's = 49,512,010 bp (26.92%) number of C's = 36,511,870 bp (19.85%) number of T's = 54,957,824 bp (29.89%) number of G's = 42,911,685 bp (23.33%) number of N's = 4,247 bp (0%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,490,040 number of insertions = 14,065 mapped reads with insertion percentage = 0.5% number of deletions = 41,948 mapped reads with deletion percentage = 1.48% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.0594X std coverageData = 0.4103X There is a 4.97% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.13% 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 13648331 0.054757460363559135 0.5365259590084578 chr2 243199373 17848356 0.07338981091863259 0.5920020686384129 chr3 198022430 13178377 0.06654992063272833 0.3038719347135205 chr4 191154276 10102482 0.05284988759550427 0.2979552629781626 chr5 180915260 9247849 0.05111702020050713 0.26070049701197606 chr6 171115067 11184160 0.06536046296846554 0.33002214001253716 chr7 159138663 11195334 0.07034955421235378 0.5582176929479598 chr8 146364022 10319175 0.0705034943628428 0.41156711746922736 chr9 141213431 10507744 0.0744103724807876 0.4966661959502375 chr10 135534747 7711309 0.05689543951411958 0.3807342711110699 chr11 135006516 6118259 0.045318249676186 0.37910982842028235 chr12 133851895 7747287 0.057879546643698994 0.285215513727903 chr13 115169878 7212725 0.06262683546473845 0.3043387067984773 chr14 107349540 4282549 0.03989350117382897 0.26546495134535814 chr15 102531392 3565093 0.03477074611451681 0.23296708905008137 chr16 90354753 6265682 0.06934535032152653 0.33851745198583083 chr17 81195210 4112730 0.050652372227376466 0.2837302879133427 chr18 78077248 3123369 0.04000357440877014 0.7599142619186454 chr19 59128983 4260849 0.07206024497326463 0.43620489312711913 chr20 63025520 7873839 0.12493096447280404 0.43772427021348076 chr21 48129895 2305530 0.04790224454052933 0.3078205601683782 chr22 51304566 2155164 0.04200725526067212 0.2500853879919597 chrMT 16571 195015 11.768450908213143 8.768656140928247 chrX 155270560 8937307 0.05755957214297417 0.31313733489935025 chrY 59373566 874429 0.014727580957492093 0.19705623956125948