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 1,882,510 T→C 39.6% P208P (CCA→CCG)  relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,882,5100TC39.6% 40.7 / 66.9 96P208P (CCA→CCG) relA(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand):  ref base T (35/23);  new base C (17/21);  total (52/44)
Fisher's exact test for biased strand distribution p-value = 1.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

Only 100 of 105 total aligned reads displayed.

CTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTA  >  minE/1882443‑1882576
                                                                   |                                                                  
ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                                                                   <  1:2942334/69‑1 (MQ=255)
ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                                                                   <  1:257554/69‑1 (MQ=255)
ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                                                                   <  1:2285505/69‑1 (MQ=255)
ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                                                                   <  1:1227256/69‑1 (MQ=255)
ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                                                                   <  1:572079/69‑1 (MQ=255)
ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                                                                   <  1:203926/69‑1 (MQ=255)
ctTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtg                                                                   <  1:1587166/69‑1 (MQ=255)
        tAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAg                                                            >  1:95214/1‑68 (MQ=255)
             ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc                                                       >  1:3058751/1‑68 (MQ=255)
             ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc                                                       >  1:303488/1‑68 (MQ=255)
             ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc                                                       >  1:2492542/1‑68 (MQ=255)
             ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc                                                       >  1:490955/1‑68 (MQ=255)
             ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc                                                       >  1:587110/1‑68 (MQ=255)
             ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc                                                       >  1:2099099/1‑68 (MQ=255)
             ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc                                                       >  1:1015467/1‑68 (MQ=255)
             ttCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAAc                                                       >  1:1232638/1‑68 (MQ=255)
                     cGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGt                                              >  1:1149590/1‑69 (MQ=255)
                     cGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGt                                              >  1:718776/1‑69 (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)
                               ttCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAg                                    <  1:130944/69‑1 (MQ=255)
                                 cATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTtgga                                                                 >  1:2985487/1‑38 (MQ=255)
                                     cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                              >  1:1214323/1‑69 (MQ=255)
                                     cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                              >  1:2261358/1‑69 (MQ=255)
                                     cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                              >  1:2380264/1‑69 (MQ=255)
                                     cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                              >  1:1940723/1‑69 (MQ=255)
                                     cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                              >  1:3377752/1‑69 (MQ=255)
                                     cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                              >  1:1388132/1‑69 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:2720051/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:3378177/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:3425352/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:1158111/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:932736/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:3250587/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:82555/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:1737417/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:1752842/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:814666/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:3357433/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:608927/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:2043337/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:1816819/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:3325428/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:676439/69‑1 (MQ=255)
                                         agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                          <  1:2676234/69‑1 (MQ=255)
                                               gCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGt                    >  1:2763577/1‑69 (MQ=255)
                                               gCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGt                    >  1:1259529/1‑69 (MQ=255)
                                               gCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGt                    >  1:2573965/1‑69 (MQ=255)
                                               gCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTACAGTTCCCATTTCAGTTg                     >  1:2082731/1‑68 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:835142/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:1852271/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:1777407/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:1704036/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:1578250/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:738331/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:2975917/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:1441499/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:3089432/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTcc                                      >  1:1417097/1‑45 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGAtt              >  1:630237/1‑69 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGAt               >  1:1879769/1‑68 (MQ=255)
                                                     cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATATTcc                                      >  1:250476/1‑45 (MQ=255)
                                                        ttGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTcc            <  1:902205/68‑1 (MQ=255)
                                                        ttGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTcc            <  1:1009684/68‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:2987386/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:866920/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:1288670/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:1329220/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:1646705/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:1938936/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:1942913/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:2014901/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:2197147/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:500972/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:368475/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:34957/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:3418686/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:2624758/54‑1 (MQ=255)
                                                         tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                         <  1:3304265/54‑1 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTgcc                   >  1:1533228/1‑52 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACgg     >  1:2009878/1‑68 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:101507/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:1057763/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:3080652/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:902143/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:3150077/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:2765971/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:13652/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:2582755/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:68216/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:2497943/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:2081028/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:2250463/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:2391988/1‑69 (MQ=255)
                                                               cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt    >  1:2384745/1‑69 (MQ=255)
                                                                  ttGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTa  <  1:2800472/68‑1 (MQ=255)
                                                                   |                                                                  
CTTCGATGTAGTGTTCGCGGTCGAGACGCCGTTCATGCAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTA  >  minE/1882443‑1882576

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