BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975298.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,600,194 number of mapped reads = 2,564,837 (98.64%) number of supplementary alignments = 29,912 (1.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,285,279 number of mapped paired reads (second in pair) = 1,279,558 number of mapped paired reads (both in pair) = 2,554,142 number of mapped paired reads (singletons) = 10,695 number of mapped bases = 343,945,749 bp number of sequenced bases = 343,708,095 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 408,774 duplication rate = 15.59% >>>>>>> Insert size mean insert size = 77,431.4768 std insert size = 2,649,449.9069 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.4735 >>>>>>> ACTG content number of A's = 100,948,462 bp (29.37%) number of C's = 68,603,698 bp (19.96%) number of T's = 101,846,087 bp (29.63%) number of G's = 72,288,027 bp (21.03%) number of N's = 21,821 bp (0.01%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 3,168,039 number of insertions = 62,681 mapped reads with insertion percentage = 2.3% number of deletions = 113,558 mapped reads with deletion percentage = 4.26% homopolymer indels = 45.97% >>>>>>> Coverage mean coverageData = 0.1111X std coverageData = 1.1894X There is a 6.01% of reference with a coverageData >= 1X There is a 3.48% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 31454464 0.12619613092157553 1.155616785594646 chr2 243199373 29312848 0.12053011337327749 1.8195369282742084 chr3 198022430 24288658 0.12265609506963428 0.5146086461335433 chr4 191154276 21727749 0.11366603695540664 1.0202524234382666 chr5 180915260 20471065 0.11315278213678603 0.4893065043938852 chr6 171115067 27680459 0.16176517641196378 0.8821660452514843 chr7 159138663 20002588 0.12569282425101183 1.0124339312396653 chr8 146364022 17408503 0.1189397692282602 0.6932591289694072 chr9 141213431 14718809 0.10423094245192584 2.4587620572627467 chr10 135534747 17278957 0.12748728560359507 1.996375606975564 chr11 135006516 12163394 0.09009486623593782 1.0398626046313144 chr12 133851895 15106609 0.11286062853275257 0.4849976426473 chr13 115169878 11099341 0.09637364554645096 0.45218843998233843 chr14 107349540 9994400 0.09310147020657937 0.46325138595266663 chr15 102531392 9602018 0.0936495429614376 0.4425193138907524 chr16 90354753 10137205 0.11219337847119122 1.2289667029028832 chr17 81195210 7170508 0.08831195830394428 1.0688851869659413 chr18 78077248 9990681 0.12795892857289232 2.2110778312652277 chr19 59128983 4672506 0.07902226222967508 0.8259522735087313 chr20 63025520 7340176 0.11646355317655452 0.5738113018582999 chr21 48129895 3990450 0.08291000842615592 0.6199804173138044 chr22 51304566 3383890 0.06595689748160037 0.37772299904533085 chrMT 16571 90191 5.442701104338905 4.223498602603733 chrX 155270560 10299996 0.06633579475722894 0.4988818728520948 chrY 59373566 4560284 0.07680663815947993 1.8512109121367584