BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618640.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 65,677,912 number of mapped reads = 51,125,044 (77.84%) number of supplementary alignments = 127,437 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,458,198 number of mapped paired reads (second in pair) = 23,666,846 number of mapped paired reads (both in pair) = 46,595,168 number of mapped paired reads (singletons) = 4,529,876 number of mapped bases = 4,816,161,946 bp number of sequenced bases = 4,812,847,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,785,543 duplication rate = 17.79% >>>>>>> Insert size mean insert size = 99,430.3399 std insert size = 3,177,155.4451 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 53.7042 >>>>>>> ACTG content number of A's = 1,304,636,675 bp (27.11%) number of C's = 1,071,409,747 bp (22.26%) number of T's = 1,335,834,884 bp (27.76%) number of G's = 1,100,746,525 bp (22.87%) number of N's = 219,320 bp (0%) GC percentage = 45.13% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 70,452,865 number of insertions = 880,468 mapped reads with insertion percentage = 1.69% number of deletions = 2,402,440 mapped reads with deletion percentage = 4.58% homopolymer indels = 52.37% >>>>>>> Coverage mean coverageData = 1.5558X std coverageData = 7.5303X There is a 25.07% of reference with a coverageData >= 1X There is a 17.07% of reference with a coverageData >= 2X There is a 12.85% of reference with a coverageData >= 3X There is a 10.26% of reference with a coverageData >= 4X There is a 8.45% of reference with a coverageData >= 5X There is a 7.13% of reference with a coverageData >= 6X There is a 6.12% of reference with a coverageData >= 7X There is a 5.32% of reference with a coverageData >= 8X There is a 4.67% of reference with a coverageData >= 9X There is a 4.13% of reference with a coverageData >= 10X There is a 3.69% of reference with a coverageData >= 11X There is a 3.31% of reference with a coverageData >= 12X There is a 2.98% of reference with a coverageData >= 13X There is a 2.7% of reference with a coverageData >= 14X There is a 2.46% of reference with a coverageData >= 15X There is a 2.24% of reference with a coverageData >= 16X There is a 2.05% of reference with a coverageData >= 17X There is a 1.88% of reference with a coverageData >= 18X There is a 1.73% of reference with a coverageData >= 19X There is a 1.6% of reference with a coverageData >= 20X There is a 1.48% of reference with a coverageData >= 21X There is a 1.37% of reference with a coverageData >= 22X There is a 1.28% of reference with a coverageData >= 23X There is a 1.19% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1.03% of reference with a coverageData >= 26X There is a 0.97% of reference with a coverageData >= 27X There is a 0.91% of reference with a coverageData >= 28X There is a 0.85% of reference with a coverageData >= 29X There is a 0.8% of reference with a coverageData >= 30X There is a 0.75% of reference with a coverageData >= 31X There is a 0.71% of reference with a coverageData >= 32X There is a 0.67% of reference with a coverageData >= 33X There is a 0.63% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.56% of reference with a coverageData >= 36X There is a 0.53% of reference with a coverageData >= 37X There is a 0.5% of reference with a coverageData >= 38X There is a 0.48% of reference with a coverageData >= 39X There is a 0.45% of reference with a coverageData >= 40X There is a 0.43% of reference with a coverageData >= 41X There is a 0.41% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.37% of reference with a coverageData >= 44X There is a 0.35% of reference with a coverageData >= 45X There is a 0.34% of reference with a coverageData >= 46X There is a 0.32% of reference with a coverageData >= 47X There is a 0.31% of reference with a coverageData >= 48X There is a 0.29% of reference with a coverageData >= 49X There is a 0.28% of reference with a coverageData >= 50X There is a 0.27% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 432318315 1.734472368676666 8.070207890888092 chr2 243199373 409605038 1.6842355839461807 8.988952430345805 chr3 198022430 304923971 1.5398456174888875 7.7656035782398805 chr4 191154276 236160293 1.235443422672899 6.041801804678766 chr5 180915260 271703502 1.5018274412009247 6.934661418154928 chr6 171115067 259032725 1.5137926165204376 6.242296094655639 chr7 159138663 243623206 1.5308863440683802 6.654451768558651 chr8 146364022 226659715 1.548602668215827 6.813478847161161 chr9 141213431 211248264 1.4959502258676798 7.482062840145315 chr10 135534747 238583802 1.760314659383988 7.161454576720919 chr11 135006516 251197549 1.8606327786430694 8.56434265208005 chr12 133851895 212032180 1.5840805242241807 7.617336038093157 chr13 115169878 125364892 1.088521531645627 5.248452455380619 chr14 107349540 149489551 1.3925495255964766 6.422650490416632 chr15 102531392 164086505 1.6003538213935493 7.28171109266513 chr16 90354753 165531525 1.8320179017035219 12.60849847643951 chr17 81195210 161398849 1.9877878140841068 8.38131714441608 chr18 78077248 121763593 1.5595272133567002 6.932642973037772 chr19 59128983 96253283 1.6278528416428202 7.163981255655944 chr20 63025520 136120251 2.1597640289203484 8.282828747001206 chr21 48129895 60491811 1.2568448570270099 8.79879215160286 chr22 51304566 91017464 1.7740616692869013 8.520167957832433 chrMT 16571 9849 0.5943515780580533 2.070718283485578 chrX 155270560 239300695 1.541185238206135 6.184961991392524 chrY 59373566 8245118 0.1388684991566786 4.397704888506691