BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094153.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 19,450 number of mapped reads = 1,035 (5.32%) number of supplementary alignments = 26 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 456 number of mapped paired reads (second in pair) = 579 number of mapped paired reads (both in pair) = 830 number of mapped paired reads (singletons) = 205 number of mapped bases = 112,893 bp number of sequenced bases = 110,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 445 duplication rate = 25.32% >>>>>>> Insert size mean insert size = 543,429.0854 std insert size = 6,547,710.0258 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 12.7273 >>>>>>> ACTG content number of A's = 25,993 bp (23.6%) number of C's = 21,194 bp (19.24%) number of T's = 24,299 bp (22.06%) number of G's = 38,659 bp (35.1%) number of N's = 0 bp (0%) GC percentage = 54.34% >>>>>>> Mismatches and indels general error rate = 0.0446 number of mismatches = 4,627 number of insertions = 85 mapped reads with insertion percentage = 6.67% number of deletions = 347 mapped reads with deletion percentage = 31.59% homopolymer indels = 33.1% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0227X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 828 3.321957621120631E-6 0.00224479283707575 chr2 243199373 19990 8.219593559560698E-5 0.07087608250398712 chr3 198022430 2656 1.3412621994387202E-5 0.006144357014581318 chr4 191154276 1666 8.715473359329927E-6 0.003715579091370877 chr5 180915260 1916 1.059059362930468E-5 0.005894527540961443 chr6 171115067 2853 1.667299116330884E-5 0.011263810528043332 chr7 159138663 3434 2.1578665644564326E-5 0.00767163250071465 chr8 146364022 448 3.060861500512742E-6 0.0021554446466751334 chr9 141213431 1465 1.0374367293717267E-5 0.005326855733753232 chr10 135534747 3415 2.519649075672086E-5 0.00816011588991796 chr11 135006516 3354 2.4843245343802517E-5 0.011646027265677962 chr12 133851895 2524 1.8856662432758235E-5 0.007913349531075966 chr13 115169878 1385 1.2025713876331449E-5 0.005282657529588064 chr14 107349540 468 4.359590176166568E-6 0.0031894134369340526 chr15 102531392 1887 1.8404119589052296E-5 0.005587432108278407 chr16 90354753 764 8.455559609575824E-6 0.00720461239202799 chr17 81195210 486 5.985574764816792E-6 0.002969549552625614 chr18 78077248 89 1.139896734065217E-6 0.0010676588568923374 chr19 59128983 535 9.048016266405258E-6 0.0037713480010732213 chr20 63025520 1557 2.4704278520827752E-5 0.009713805024370843 chr21 48129895 31 6.440903309678943E-7 8.025521267279402E-4 chr22 51304566 0 0.0 0.0 chrMT 16571 3815 0.230221471244946 1.1193107619159537 chrX 155270560 55896 3.599909731761127E-4 0.03888691024062 chrY 59373566 1431 2.410163472411275E-5 0.010719099262289252