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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,882,471 C→G 41.4% R221R (CGG→CGC)  relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,882,4710CG41.4% 45.5 / 85.6 87R221R (CGG→CGC) relA(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand):  ref base C (37/14);  new base G (30/6);  total (67/20)
Fisher's exact test for biased strand distribution p-value = 3.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CCTTCAGCTTTCATCTCAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAA  >  minE/1882403‑1882534
                                                                    |                                                               
ccTTCAGCTTTCATCTCAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGc                                                                 >  1:108994/1‑69 (MQ=255)
ccTTCAGCTTTCATCTCAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGc                                                                 <  1:1117741/69‑1 (MQ=255)
ccTTCAGCTTTCATCTCAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGc                                                                 <  1:2852946/69‑1 (MQ=255)
ccTTCAGCTTTCATCTCAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGc                                                                 <  1:2230276/69‑1 (MQ=255)
ccTTCAGCTTTCATCTCAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGc                                                                 >  1:1261153/1‑69 (MQ=255)
ccTTCAGCTTTCATCTCAGCGCGCAGATGACCAACGAACTCATCGATGTAGTGTTCGCGGTCGAGACGc                                                                 >  1:1001572/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:2498353/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:993432/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:813199/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:784297/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:3425598/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:326354/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:2982266/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:2127774/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:1826230/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:1282195/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:1094103/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTc                                                            >  1:1162218/1‑69 (MQ=255)
     aGCTTTCATCTCAGCGCGCAGATGGCCGACAAACTCTTCGATATAGTGTTCGAGGTCGAGACGGCGTTc                                                            >  1:1476047/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTGGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGcagcag                                                   >  1:408954/1‑68 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGCCGCCGTTc                                                            >  1:1434567/1‑59 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGcagcag                                                   >  1:2889483/1‑68 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:2536300/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:3230208/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:2204763/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:3045225/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:2382615/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:2397043/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:2464144/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:97862/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:3003315/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:2648128/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:2789928/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:2917197/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:1468726/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:177649/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:1753290/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:1726956/1‑69 (MQ=255)
               tcAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGt                                                  >  1:1731405/1‑69 (MQ=255)
                    gcgcAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGc                                             <  1:462879/69‑1 (MQ=255)
                     cgcAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGc                                             <  1:931889/68‑1 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:3033302/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:2918376/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:1499234/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:2685614/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:40370/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:2953200/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:2527941/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:1744934/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:1960610/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:1748761/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:105451/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:609138/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:1953317/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:3137745/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCgg                            >  1:1958920/1‑69 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCg                             >  1:494796/1‑68 (MQ=255)
                                     aCTCTTCGATATAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGACGCGTTTGTATTCgg                            >  1:1684632/1‑69 (MQ=255)
                                      ctctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGt                           >  1:1026804/1‑69 (MQ=255)
                                      ctctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGt                           >  1:44130/1‑69 (MQ=255)
                                      ctctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGt                           >  1:2556375/1‑69 (MQ=255)
                                      ctctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGt                           >  1:1020897/1‑69 (MQ=255)
                                      ctctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGt                           >  1:3075952/1‑69 (MQ=255)
                                        ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                         <  1:2942334/69‑1 (MQ=255)
                                        ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                         <  1:572079/69‑1 (MQ=255)
                                        ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                         <  1:1587166/69‑1 (MQ=255)
                                        ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                         <  1:203926/69‑1 (MQ=255)
                                        ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                         <  1:1227256/69‑1 (MQ=255)
                                        ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                         <  1:2285505/69‑1 (MQ=255)
                                        ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                         <  1:257554/69‑1 (MQ=255)
                                              tatAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCGGtc                          <  1:1831722/60‑2 (MQ=255)
                                              tatAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCGGtc                          <  1:3365970/60‑2 (MQ=255)
                                              tatAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCGGtc                          <  1:1258621/60‑2 (MQ=255)
                                              tatAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCGGtc                          <  1:635111/60‑2 (MQ=255)
                                              tatAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATGCGTTTGTATTCGGtc                          <  1:695325/60‑2 (MQ=255)
                                              tatAGTGTTCGCGGTCGAGACGGCGTTCATGCAGCAGTTTTGCGATACGTTTGTATTCGGtc                          <  1:1335950/60‑2 (MQ=255)
                                                tAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAg                  >  1:95214/1‑68 (MQ=255)
                                                     ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc             >  1:587110/1‑68 (MQ=255)
                                                     ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc             >  1:1015467/1‑68 (MQ=255)
                                                     ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc             >  1:490955/1‑68 (MQ=255)
                                                     ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc             >  1:3058751/1‑68 (MQ=255)
                                                     ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc             >  1:303488/1‑68 (MQ=255)
                                                     ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc             >  1:2492542/1‑68 (MQ=255)
                                                     ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc             >  1:1232638/1‑68 (MQ=255)
                                                     ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc             >  1:2099099/1‑68 (MQ=255)
                                                             cGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGt    >  1:718776/1‑69 (MQ=255)
                                                             cGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGt    >  1:1149590/1‑69 (MQ=255)
                                                             cGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGt    >  1:2202785/1‑69 (MQ=255)
                                                              gagaCGCCGTTCATGCAGCAGTTTGTCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTa   <  1:3299596/69‑1 (MQ=255)
                                                              gagaCGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTa   <  1:727243/69‑1 (MQ=255)
                                                              gagaCGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTa   <  1:1889420/69‑1 (MQ=255)
                                                                gaCGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTaa  <  1:111208/68‑1 (MQ=255)
                                                                 aCGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTaa  <  1:704680/67‑1 (MQ=255)
                                                                    |                                                               
CCTTCAGCTTTCATCTCAGCGCGCAGATGACCAACGAACTCTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAA  >  minE/1882403‑1882534

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A