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 2,039,441 A→G 27.1% I158I (ATT→ATC)  ribB ← 3,4 dihydroxy‑2‑butanone‑4‑phosphate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,039,4410AG27.1% 111.6 / 42.1 103I158I (ATT→ATC) ribB3,4 dihydroxy‑2‑butanone‑4‑phosphate synthase
Reads supporting (aligned to +/- strand):  ref base A (36/39);  new base G (18/10);  total (54/49)
Fisher's exact test for biased strand distribution p-value = 1.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 103 total aligned reads displayed.

CCATCGTCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGAGCGCGAAGTGGGAAAA  >  minE/2039376‑2039505
                                                                 |                                                                
ccatcgtCATTAGTCAGCTCACTCAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATa                                                               >  1:3165614/1‑69 (MQ=255)
ccatcgtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATa                                                               >  1:1927958/1‑69 (MQ=255)
ccatcgtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATa                                                               >  1:1044018/1‑69 (MQ=255)
ccatcgtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATa                                                               >  1:1105718/1‑69 (MQ=255)
ccatcgtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATa                                                               >  1:1649366/1‑69 (MQ=255)
ccatcgtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATa                                                               >  1:2746702/1‑69 (MQ=255)
ccatcgtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATa                                                               >  1:2789067/1‑69 (MQ=255)
ccatcgtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATa                                                               >  1:3072632/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:3062168/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:2362080/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:1698005/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:26208/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:1462779/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:423965/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:1059016/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:6027/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:517905/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:43138/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:1264643/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:1196925/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:419976/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:404128/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGACAGCGTCATCAGATCAATAGTTGc                                                          >  1:2527239/1‑69 (MQ=255)
     gtCATTAGTCAGCTCACACAGCACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGc                                                          >  1:136824/1‑69 (MQ=255)
          tAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     <  1:2629039/69‑1 (MQ=255)
          tAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     <  1:2483622/69‑1 (MQ=255)
          tAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     >  1:2397273/1‑69 (MQ=255)
          tAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     <  1:294180/69‑1 (MQ=255)
          tAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     >  1:942460/1‑69 (MQ=255)
          tAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     <  1:2006457/69‑1 (MQ=255)
          tAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     <  1:1526684/69‑1 (MQ=255)
          tAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     <  1:1088894/69‑1 (MQ=255)
           aGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     <  1:2966667/68‑1 (MQ=255)
           aGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGt                                                    >  1:720559/1‑69 (MQ=255)
              cAGCTCACACAGTACACCAGCCTGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTAtt                                                 <  1:1746555/69‑2 (MQ=255)
              cAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATg                                                 <  1:1262232/69‑1 (MQ=255)
              cAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATg                                                 <  1:1407863/69‑1 (MQ=255)
                   cacacaGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGc                                            <  1:2559759/69‑1 (MQ=255)
                    acacaGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGc                                            <  1:2849459/68‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:342002/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:1433078/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:2914886/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:1083583/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:37254/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:1244698/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:1178563/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:795059/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:2262535/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:2263251/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:1552889/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:2155154/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:2073492/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:196988/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:1735919/69‑1 (MQ=255)
                           acacCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTc                                    <  1:2265927/69‑1 (MQ=255)
                              ccAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATTAATAGTTGCTTCAGTATGACCGCCACGCGTCAg                                  <  1:1423661/68‑1 (MQ=255)
                              ccAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAg                                  <  1:1909524/68‑1 (MQ=255)
                              ccAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAg                                  <  1:3089878/68‑1 (MQ=255)
                              ccAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAg                                  <  1:2357450/68‑1 (MQ=255)
                              ccAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAg                                  <  1:1422315/68‑1 (MQ=255)
                              ccAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAg                                  <  1:805594/68‑1 (MQ=255)
                              ccAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAg                                  <  1:2556275/68‑1 (MQ=255)
                              ccAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAg                                  <  1:815406/68‑1 (MQ=255)
                                      tttAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAg                                                     <  1:262626/41‑1 (MQ=255)
                                       ttAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGc                                            <  1:65531/49‑1 (MQ=255)
                                                         atcaGATCAATAGTTGCTTCAGTATGACCGCCAcgc                                       >  1:2033998/1‑36 (MQ=255)
                                                         atcaGATCAATAGTTGCTTCAGTATGACCGCCAcgc                                       >  1:427933/1‑36 (MQ=255)
                                                         atcaGATCAATAGTTGCTTCAGTATGACCGCCAcgc                                       >  1:40483/1‑36 (MQ=255)
                                                         atcaGATCAATAGTTGCTTCAGTATGACCGCCAcgc                                       >  1:2499151/1‑36 (MQ=255)
                                                         atcaGATCAATAGTTGCTTCAGTATGACCGCCAcgc                                       >  1:1540101/1‑36 (MQ=255)
                                                         atcaGATCAATAGTTGCTTCAGTATGACCGCCAcgc                                       >  1:1504813/1‑36 (MQ=255)
                                                         atcaGATCAATAGTTGCTTCAGTATGACCGCCAcgc                                       >  1:1417289/1‑36 (MQ=255)
                                                         atcaGATCAATAGTTGCTTCAGTATGACCGCCAcg                                        >  1:2188271/1‑35 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGCCCGCCACGCGTCAGTACACCACCTGCCTgcgca               >  1:644066/1‑55 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGa            >  1:3205240/1‑59 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGt         >  1:512270/1‑62 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTg        >  1:2357946/1‑63 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:3166001/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:2482290/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:697736/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:546245/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:522846/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:470323/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:3123109/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:3217824/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:3051977/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:2114579/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:1275433/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:1259955/1‑69 (MQ=255)
                                                             gATCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAACTGGGaaaa  >  1:3054708/1‑69 (MQ=255)
                                                             gATCGAAAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  >  1:435884/1‑69 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:1084050/68‑1 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:3327770/68‑1 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:2628769/68‑1 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:2176274/68‑1 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:44283/68‑1 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:3015684/68‑1 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:1112096/68‑1 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:501995/68‑1 (MQ=255)
                                                              aTCGATAGTCGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGCGCACGAAGTGGGaaaa  <  1:466737/68‑1 (MQ=255)
                                                                 |                                                                
CCATCGTCATTAGTCAGCTCACACAGTACACCAGCCGGTTTAAAGCCTGCCAGCGTCATCAGATCAATAGTTGCTTCAGTATGACCGCCACGCGTCAGTACACCACCTGCCTGAGCGCGAAGTGGGAAAA  >  minE/2039376‑2039505

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