BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081035.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 = 1,855,323 number of mapped reads = 1,511,544 (81.47%) number of supplementary alignments = 8,660 (0.47%) number of secondary alignments = 0 number of mapped bases = 97,168,040 bp number of sequenced bases = 97,134,327 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,127 duplication rate = 1.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9516 >>>>>>> ACTG content number of A's = 29,100,795 bp (29.96%) number of C's = 18,701,171 bp (19.25%) number of T's = 28,664,385 bp (29.51%) number of G's = 20,666,725 bp (21.28%) number of N's = 1,251 bp (0%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 758,439 number of insertions = 6,570 mapped reads with insertion percentage = 0.43% number of deletions = 19,799 mapped reads with deletion percentage = 1.3% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.2485X There is a 2.77% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8895090 0.03568733335272212 0.3913339386427079 chr2 243199373 7769326 0.031946324137932705 0.26509537191222143 chr3 198022430 7337020 0.03705145927155828 0.21297908664068807 chr4 191154276 5657925 0.02959873625845545 0.19827876208045192 chr5 180915260 5758312 0.03182877994924253 0.19722055347320402 chr6 171115067 6006753 0.035103589095400935 0.23674466827698742 chr7 159138663 5046060 0.03170857354758598 0.273914254736929 chr8 146364022 4686636 0.03202041004311838 0.28725239918452505 chr9 141213431 4440400 0.031444601045066314 0.23700397404981674 chr10 135534747 4499331 0.03319688197743122 0.24429658761808332 chr11 135006516 4254609 0.03151410114160712 0.23473363872245998 chr12 133851895 4715197 0.0352269723189201 0.20891890747090822 chr13 115169878 3027656 0.026288609943652105 0.1781008953057461 chr14 107349540 2514319 0.023421795752455017 0.17447757581736034 chr15 102531392 2618820 0.025541640944463137 0.17919125724797463 chr16 90354753 3015061 0.03336914661257499 0.2147399426175942 chr17 81195210 2441485 0.030069323054894494 0.2023366734550538 chr18 78077248 2656263 0.034020960882227815 0.4104503840506781 chr19 59128983 1629688 0.02756157669750552 0.2795788988482496 chr20 63025520 1934792 0.03069854877833614 0.19745924583086147 chr21 48129895 1015561 0.02110042001961567 0.17228318523048985 chr22 51304566 992847 0.01935202024708678 0.15271535152363844 chrMT 16571 37222 2.2462132641361414 2.061145331641249 chrX 155270560 5980789 0.038518499579057355 0.2280178234684632 chrY 59373566 236878 0.00398962056616239 0.09195573530833373