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 1,567,424 T→C 34.5% L392L (CTT→CTC)  yfeO → predicted ion channel protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,567,4240TC34.5% 120.8 / 100.7 168L392L (CTT→CTC) yfeOpredicted ion channel protein
Reads supporting (aligned to +/- strand):  ref base T (46/64);  new base C (30/28);  total (76/92)
Fisher's exact test for biased strand distribution p-value = 2.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01

Only 100 of 168 total aligned reads displayed.

TTTTTATGGCGGCAGTCGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGCAACAGC  >  minE/1567360‑1567485
                                                                |                                                             
tttttATGGCGGCAGTCGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCgg                                                           <  1:2488997/69‑1 (MQ=255)
tttttATGGCGGCAGTCGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCgg                                                           <  1:1981442/69‑1 (MQ=255)
tttttATGGCGGCAGTCGTTGTACCCAATACCACATTGCTACAGCTGCTCTGTATCGTCATGCTTCCgg                                                           <  1:1117266/69‑1 (MQ=255)
    tATGGCGGCAGTCGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGc                                                          <  1:1883830/66‑1 (MQ=255)
                cGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGc                                           >  1:2750165/1‑69 (MQ=255)
                cGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGc                                           >  1:2364646/1‑69 (MQ=255)
                cGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGc                                           >  1:505384/1‑69 (MQ=255)
                cGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGc                                           >  1:1132941/1‑69 (MQ=255)
                cGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGc                                           >  1:3191090/1‑69 (MQ=255)
                    gTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGt                                                  >  1:3424326/1‑58 (MQ=255)
                    gTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGt                                                  >  1:2933140/1‑58 (MQ=255)
                    gTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGt                                                  >  1:2269242/1‑58 (MQ=255)
                    gTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGt                                                  >  1:1936856/1‑58 (MQ=255)
                    gTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGt                                                  >  1:1552547/1‑58 (MQ=255)
                    gTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGt                                                  >  1:1084537/1‑58 (MQ=255)
                    gTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGt                                                  >  1:1091646/1‑58 (MQ=255)
                       cccAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAg                                    <  1:3306955/69‑1 (MQ=255)
                       cccAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAg                                    <  1:2889404/69‑1 (MQ=255)
                       cccAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAg                                    <  1:2730326/69‑1 (MQ=255)
                       cccAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAg                                    <  1:107599/69‑1 (MQ=255)
                       cccAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAg                                    <  1:774963/69‑1 (MQ=255)
                       cccAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAg                                    <  1:726052/69‑1 (MQ=255)
                         ctaTACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGcc                                  <  1:2871850/67‑1 (MQ=255)
                              ccACATTGCTACCTCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGcc                                  <  1:1352462/64‑1 (MQ=255)
                              ccACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGcc                                  <  1:482041/64‑1 (MQ=255)
                              ccACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGcc                                  <  1:1040005/64‑1 (MQ=255)
                              ccACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCgatg                              >  1:2546269/1‑68 (MQ=255)
                              ccACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCgat                               >  1:3292088/1‑67 (MQ=255)
                                acaTTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgat                            <  1:2641941/68‑1 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:694116/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:235782/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:1450052/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:2443305/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:2935860/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:1318857/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:2135756/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:2096169/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:1453015/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:2686634/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:1881823/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:386165/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:747613/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:1743089/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:2802643/1‑69 (MQ=255)
                                 caTTGCTACCGCTGCTCTGTATCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCgatgatga                          >  1:3206059/1‑69 (MQ=255)
                                    tGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGatgatgatg                        >  1:3221550/1‑68 (MQ=255)
                                    tGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGatgatgatg                        >  1:1409907/1‑68 (MQ=255)
                                    tGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGatgatgatg                        >  1:697874/1‑68 (MQ=255)
                                     gCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATgg                       >  1:2289901/1‑68 (MQ=255)
                                     gCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATgg                       >  1:1662053/1‑68 (MQ=255)
                                     gCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATgg                       >  1:2731957/1‑68 (MQ=255)
                                     gCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATCGCTGTTATTAGCAGGTAAGCCGATGATGATgg                       >  1:3320878/1‑68 (MQ=255)
                                        aCCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGcc                                  >  1:2163585/1‑54 (MQ=255)
                                        aCCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCaa                   >  1:152791/1‑69 (MQ=255)
                                        aCCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCaa                   >  1:1185281/1‑69 (MQ=255)
                                        aCCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCaa                   >  1:2602461/1‑69 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:2537167/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:2554482/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:3075442/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:2186080/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:145997/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:2257806/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:521201/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:793549/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:2772143/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:1701595/69‑1 (MQ=255)
                                             tgctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:3271375/69‑1 (MQ=255)
                                              gctCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTc              <  1:2300960/68‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:3348567/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:2906683/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:2846455/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:1975435/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:1755509/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:1533814/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:1493243/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:1472555/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:1393922/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGc        <  1:879411/66‑1 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGCAAc     >  1:259196/1‑69 (MQ=255)
                                                      tCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGCAAc     >  1:89196/1‑69 (MQ=255)
                                                      tCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGc        <  1:362808/66‑1 (MQ=255)
                                                      tCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGc        <  1:585967/66‑1 (MQ=255)
                                                      tCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGc        <  1:962128/66‑1 (MQ=255)
                                                      tCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGc        <  1:2334795/66‑1 (MQ=255)
                                                      tCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGc        <  1:2263592/66‑1 (MQ=255)
                                                      tCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGc        <  1:1072810/66‑1 (MQ=255)
                                                      tCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGc        <  1:1147469/66‑1 (MQ=255)
                                                      tCGTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGc        <  1:334077/66‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:1474091/68‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:1001105/68‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:106983/68‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:857067/68‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:1416534/68‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:1640454/68‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:1777788/68‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:2305587/68‑1 (MQ=255)
                                                        gTCATGCTCCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:24992/68‑1 (MQ=255)
                                                         tCATGCTCCCGGCATGGCTGTTATTACCAGGTAAGCCGATGATGATGGTCAATCGTCAGAAGCAACa    <  1:1258347/67‑1 (MQ=255)
                                                          cATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGCAACAGc  <  1:1635759/68‑1 (MQ=255)
                                                          cATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGGCAATCGTCCGAAGCAACAGc  <  1:1021201/68‑1 (MQ=255)
                                                                |                                                             
TTTTTATGGCGGCAGTCGTTGTACCCAATACCACATTGCTACCGCTGCTCTGTATCGTCATGCTTCCGGCATGGCTGTTATTAGCAGGTAAGCCGATGATGATGGTCAATCGTCCGAAGCAACAGC  >  minE/1567360‑1567485

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