BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085127.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 = 1,124,314 number of mapped reads = 991,381 (88.18%) number of supplementary alignments = 7,609 (0.68%) number of secondary alignments = 0 number of mapped bases = 66,374,078 bp number of sequenced bases = 66,348,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,921 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7023 >>>>>>> ACTG content number of A's = 18,719,610 bp (28.21%) number of C's = 12,407,821 bp (18.7%) number of T's = 20,407,642 bp (30.76%) number of G's = 14,798,965 bp (22.3%) number of N's = 14,345 bp (0.02%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 594,929 number of insertions = 5,743 mapped reads with insertion percentage = 0.57% number of deletions = 15,490 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.0214X std coverageData = 0.2329X There is a 1.98% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% 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 5259664 0.021101909310789643 0.3688996876531875 chr2 243199373 5640143 0.023191437257529444 0.28687160826929475 chr3 198022430 4470299 0.022574710349731592 0.15869563435305098 chr4 191154276 4436347 0.023208201735440123 0.16544200761282568 chr5 180915260 4124660 0.022798850688438333 0.16016624736851584 chr6 171115067 3893788 0.02275537781836593 0.18192624931044604 chr7 159138663 3744633 0.02353063001415313 0.3221014452397843 chr8 146364022 3410194 0.023299400722945424 0.3305545200096732 chr9 141213431 2801501 0.019838771568406972 0.23413369289154576 chr10 135534747 3055914 0.022547088976378877 0.20909665670721386 chr11 135006516 2991356 0.0221571231421156 0.21197673844178172 chr12 133851895 2992999 0.022360527656332396 0.15988868213660284 chr13 115169878 2140034 0.018581542649545917 0.1438904762059606 chr14 107349540 2013226 0.018753932247869903 0.15567984686528133 chr15 102531392 1848147 0.01802518198524019 0.14329342505558615 chr16 90354753 1826739 0.020217409038791795 0.16564392873297182 chr17 81195210 1694050 0.0208639154945224 0.16640308617005936 chr18 78077248 1823464 0.02335461413803929 0.3888769384623059 chr19 59128983 1253745 0.02120356103537245 0.29220126204599145 chr20 63025520 1301941 0.020657362287530512 0.15576811470313542 chr21 48129895 843804 0.017531806375226874 0.14642433185395323 chr22 51304566 676369 0.013183407496323038 0.12082018854590829 chrMT 16571 2997 0.18085812564118037 0.4459141511282363 chrX 155270560 3952951 0.025458470684977242 0.18735248917516475 chrY 59373566 175113 0.0029493428102330926 0.07903027153853455