Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,198,825 G→A 80.4% A398T (GCG→ACG)  metG → methionyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,198,8250GA80.4% 120.7 / 25.3 56A398T (GCG→ACG) metGmethionyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base G (7/4);  new base A (33/12);  total (40/16)
Fisher's exact test for biased strand distribution p-value = 7.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GAAGATTTCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCTGACCCGCAGT  >  W3110S.gb/2198759‑2198885
                                                                  |                                                            
gAAGATTTCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACg                                                            >  1:1873281/1‑69 (MQ=255)
   gATTTCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGc                                                         >  1:366768/1‑69 (MQ=255)
   gATTTCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGc                                                         >  1:3108334/1‑69 (MQ=255)
      ttCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCttt                                                      >  1:1616369/1‑69 (MQ=255)
      ttCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCttt                                                      >  1:377830/1‑69 (MQ=255)
      ttCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCtt                                                       >  1:2372205/1‑68 (MQ=255)
       tCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTa                                                     <  1:1458615/69‑1 (MQ=255)
          ttCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATc                                                   <  1:1099835/68‑1 (MQ=255)
          ttCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATc                                                   <  1:1369478/68‑1 (MQ=255)
                 tgtgAATGCCGACATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCg                                           <  1:775872/69‑1 (MQ=255)
                   tgAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtt                                         >  1:3269585/1‑69 (MQ=255)
                     aaTGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGtttt                                       <  1:3150751/69‑1 (MQ=255)
                     aaTGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       >  1:1968507/1‑69 (MQ=255)
                     aaTGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       >  1:2129005/1‑69 (MQ=255)
                     aaTGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       <  1:2841772/69‑1 (MQ=255)
                     aaTGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       >  1:1133892/1‑69 (MQ=255)
                           gATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGActg                                  <  1:870576/68‑3 (MQ=255)
                             tatCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGt                               <  1:3262840/69‑1 (MQ=255)
                              atCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       >  1:97115/1‑60 (MQ=255)
                              atCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       >  1:1495239/1‑60 (MQ=255)
                              atCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtt                                         >  1:213462/1‑58 (MQ=255)
                              atCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTg                              >  1:273695/1‑69 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCt                            >  1:1800542/1‑68 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCt                            >  1:1274463/1‑68 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCt                            >  1:742179/1‑68 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCt                            >  1:327118/1‑68 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       <  1:2647915/57‑1 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       <  1:1379830/57‑1 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       <  1:1833790/57‑1 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       <  1:694486/57‑1 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtt                                         >  1:291911/1‑55 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtt                                         >  1:3404063/1‑55 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtt                                         >  1:694314/1‑55 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtt                                         >  1:1706308/1‑55 (MQ=255)
                                 gTTAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCt                            >  1:1903805/1‑68 (MQ=255)
                                 gTTAACAAAGTGGTGAACCTGGCATCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCt                            >  1:1676009/1‑68 (MQ=255)
                                   tAACAAAGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGc                         <  1:2575431/69‑1 (MQ=255)
                                        aaGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCg                    <  1:46142/69‑1 (MQ=255)
                                        aaGTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCg                    <  1:2892700/69‑1 (MQ=255)
                                         aGTGGTTAACCTGGCCTCACGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGa                   <  1:3661474/69‑1 (MQ=255)
                                          gTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGt                                          >  1:3128283/1‑45 (MQ=255)
                                          gTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGt                                          >  1:2510271/1‑45 (MQ=255)
                                          gTGGTTAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGAGt                                          >  1:284393/1‑45 (MQ=38)
                                               tAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTgg              >  1:2415618/1‑68 (MQ=255)
                                               tAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       >  1:843716/1‑43 (MQ=255)
                                               tAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       >  1:3387345/1‑43 (MQ=255)
                                               tAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGtttt                                       >  1:2007434/1‑43 (MQ=255)
                                               tAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTgg              >  1:934563/1‑68 (MQ=255)
                                               tAACCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTgg              >  1:211772/1‑68 (MQ=255)
                                                aaCCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCt            >  1:246158/1‑69 (MQ=255)
                                                aaCCTGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCt            >  1:1840985/1‑69 (MQ=255)
                                                    tGGCCTCCCGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCTGAcc        >  1:2130424/1‑69 (MQ=255)
                                                      gCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCTGAcc        >  1:1669022/1‑67 (MQ=255)
                                                           ccGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCTGACCCGCAGt  >  1:1702743/1‑68 (MQ=255)
                                                           ccGTAATACGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCTGACCCGCAGt  >  1:184057/1‑68 (MQ=255)
                                                           ccGTAATACGGGCGTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCTGACCCGCAg   >  1:3468305/1‑67 (MQ=255)
                                                                  |                                                            
GAAGATTTCGTTCAGCGTGTGAATGCCGATATCGTTAACAAAGTGGTTAACCTGGCCTCCCGTAATGCGGGCTTTATCAACAAGCGTTTTGACGGCGTGCTGGCAAGCGAACTGGCTGACCCGCAGT  >  W3110S.gb/2198759‑2198885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A