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 526,404 T→G 55.7% A22A (GCT→GCG)  ybhL → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE526,4040TG55.7% 49.6 / 102.2 106A22A (GCT→GCG) ybhLpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (32/15);  new base G (18/41);  total (50/56)
Fisher's exact test for biased strand distribution p-value = 1.75e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 106 total aligned reads displayed.

ATGGACAGATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTATGCGGCTAAT  >  minE/526339‑526470
                                                                 |                                                                  
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:811006/69‑1 (MQ=255)
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:791108/69‑1 (MQ=255)
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:1110134/69‑1 (MQ=255)
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:2013531/69‑1 (MQ=255)
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:2012467/69‑1 (MQ=255)
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:336155/69‑1 (MQ=255)
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:517456/69‑1 (MQ=255)
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:523172/69‑1 (MQ=255)
aTGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:567071/69‑1 (MQ=255)
 tGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:2280362/68‑1 (MQ=255)
 tGGACAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCaa                                                                 <  1:1594502/68‑1 (MQ=255)
   gACAGATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTc                                                              >  1:232178/1‑69 (MQ=255)
   gACAGATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTc                                                              >  1:622015/1‑69 (MQ=255)
    aCAGATTCCGACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCAAGTCt                                                             >  1:1122886/1‑69 (MQ=255)
    aCAGATTCCCACGTTCTGATTCAATTGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCGCAAGTCt                                                             >  1:1235117/1‑69 (MQ=255)
      aGATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTAt                                                           >  1:458216/1‑69 (MQ=255)
       gATTCCCACGTTCTGATTCAATCTTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATg                                                          >  1:818813/1‑69 (MQ=255)
       gATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATg                                                          >  1:1584778/1‑69 (MQ=255)
       gATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATg                                                          >  1:388711/1‑69 (MQ=255)
       gATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATg                                                          >  1:150780/1‑69 (MQ=255)
       gATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATg                                                          >  1:1927601/1‑69 (MQ=255)
       gATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATg                                                          >  1:2100281/1‑69 (MQ=255)
       gATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATg                                                          >  1:2812402/1‑69 (MQ=255)
           cccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:2525913/69‑1 (MQ=255)
           cccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:383528/69‑1 (MQ=255)
           cccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:1686671/69‑1 (MQ=255)
           cccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:3164949/69‑1 (MQ=255)
           cccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:3151033/69‑1 (MQ=255)
           cccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:578293/69‑1 (MQ=255)
           cccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:1190679/69‑1 (MQ=255)
           cccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:776621/69‑1 (MQ=255)
            ccACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTg                                                      <  1:607080/68‑1 (MQ=255)
                             cGTACAGCCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGa                                                    >  1:437556/1‑53 (MQ=255)
                             cGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATg                                                  >  1:2821467/1‑55 (MQ=255)
                             cGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATg                                                  >  1:2333295/1‑55 (MQ=255)
                                 cAACCCCGGGCTGTCTTGCAAACTTATATGGCTCAAGTc                                                              >  1:2644884/1‑39 (MQ=255)
                                 cAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTc                                                              >  1:2778308/1‑39 (MQ=255)
                                 cAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTc                                                              >  1:2686398/1‑39 (MQ=255)
                                 cAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTc                                                              >  1:2964823/1‑39 (MQ=255)
                                 cAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTc                                                              >  1:493553/1‑39 (MQ=255)
                                 cAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTc                                                              >  1:1004203/1‑39 (MQ=255)
                                 cAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTg                                >  1:760283/1‑69 (MQ=255)
                                 cAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTg                                >  1:1352842/1‑69 (MQ=255)
                                 cAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTg                                >  1:871967/1‑69 (MQ=255)
                                     cccGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCg                            <  1:2350475/69‑1 (MQ=255)
                                     cccGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCg                            <  1:2430665/69‑1 (MQ=255)
                                     cccGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCg                            <  1:349921/69‑1 (MQ=255)
                                             ggctTGCAATCTTATATGGCTCAAGTCTATGGCTg                                                      <  1:673845/35‑1 (MQ=255)
                                             ggctTGCAAACTTATATGGCGGAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:1255468/69‑1 (MQ=255)
                                             ggctTGCAAACTTATATGGCGCAAGTCTATGTCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:661276/69‑1 (MQ=255)
                                             ggctTGCAAACTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:2934686/69‑1 (MQ=255)
                                             ggctTGCAAACTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:3244771/69‑1 (MQ=255)
                                             ggctTGCAAACTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:2905337/69‑1 (MQ=255)
                                             ggctTGCAAACTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:1622540/69‑1 (MQ=255)
                                             ggctTGCAAACTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:2098860/69‑1 (MQ=255)
                                             ggctTGCAAACTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:2522709/69‑1 (MQ=255)
                                              gctTGCAAACTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:161358/68‑1 (MQ=255)
                                              gctTGCAAACTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttgtt                    <  1:2579531/68‑1 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGTCttgtt                                    >  1:615648/1‑45 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGt             >  1:2267914/1‑68 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:3034861/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:807486/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:2377570/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:1210866/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:2262591/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:1275061/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:1463324/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:1599265/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:915702/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:3416478/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:3362822/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:3238962/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:3125112/1‑69 (MQ=255)
                                                     aaCTTATATGGCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTa            >  1:1753474/1‑69 (MQ=255)
                                                              ggCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:2400449/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:1937428/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:106837/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:1130104/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:2309543/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:3114901/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:2417701/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:1233935/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:1913030/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:13427/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:1351335/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:2158045/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:47893/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:1749242/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:1613517/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:2088483/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:2934671/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATttg                      <  1:2029095/50‑1 (MQ=255)
                                                              ggCGCAAGTCTATGGCTGGATGACCGTTGGCTTGTTCCTGACCGCATttg                      <  1:626232/50‑1 (MQ=255)
                                                               gCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCAtt                        >  1:3310948/1‑47 (MQ=255)
                                                               gCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTATGCGGCTaa   >  1:1057210/1‑68 (MQ=255)
                                                               gCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTATGCGGCTAAt  >  1:3131704/1‑69 (MQ=255)
                                                               gCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTATGCGGCTAAt  >  1:272120/1‑69 (MQ=255)
                                                               gCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTATGCGGCTAAt  >  1:2058151/1‑69 (MQ=255)
                                                               gCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTATGCGGCTAAt  >  1:994592/1‑69 (MQ=255)
                                                               gCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTATGCGGCTAAt  >  1:998804/1‑69 (MQ=255)
                                                                 |                                                                  
ATGGACAGATTCCCACGTTCTGATTCAATCGTACAACCCCGGGCTGGCTTGCAAACTTATATGGCTCAAGTCTATGGCTGGATGACCGTTGGCTTGTTGCTGACCGCATTTGTTGCCTGGTATGCGGCTAAT  >  minE/526339‑526470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A