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 941,252 A→C 29.9% V44V (GTT→GTG)  bdm ← biofilm‑dependent modulation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE941,2520AC29.9% 125.8 / 86.0 124V44V (GTT→GTG) bdmbiofilm‑dependent modulation protein
Reads supporting (aligned to +/- strand):  ref base A (43/44);  new base C (20/17);  total (63/61)
Fisher's exact test for biased strand distribution p-value = 6.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01

Only 100 of 124 total aligned reads displayed.

GACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCCGAAGGC  >  minE/941192‑941316
                                                            |                                                                
gACCACATAATTGATCGTTTGCTGGTAGATATCAGTGAGGATGTCGTTATCAGAAGCTTCAACCCAttt                                                          >  1:1047719/1‑69 (MQ=255)
gACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCAttt                                                          >  1:2810067/1‑69 (MQ=255)
gACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCAttt                                                          >  1:415186/1‑69 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCAtt                                                           >  1:1116107/1‑59 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCt                                                  >  1:968961/1‑68 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc                                                 >  1:320790/1‑69 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc                                                 >  1:1394071/1‑69 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc                                                 >  1:1332698/1‑69 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc                                                 >  1:2202501/1‑69 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc                                                 >  1:379937/1‑69 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc                                                 >  1:499342/1‑69 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc                                                 >  1:691116/1‑69 (MQ=255)
         aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATATGGTCAGCt                                                  >  1:857775/1‑68 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:360511/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:1033055/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:2910603/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:2366961/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:500697/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:2151604/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:2014306/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:1932102/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:177738/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:1660053/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:1303556/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:1332448/69‑1 (MQ=255)
               cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:1262154/69‑1 (MQ=255)
                gTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgaga                                          >  1:1625992/1‑69 (MQ=255)
                gTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgaga                                          >  1:3050806/1‑69 (MQ=255)
                gTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgaga                                          >  1:1110337/1‑69 (MQ=255)
                gTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           <  1:2681207/68‑1 (MQ=255)
                gTTTGCTGGGAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgaga                                          >  1:1534419/1‑69 (MQ=255)
                           gATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCAATGAGAATGTCATCtt                                <  1:3069367/68‑1 (MQ=255)
                              atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            <  1:1840150/69‑1 (MQ=255)
                              atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            <  1:2857808/69‑1 (MQ=255)
                              atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            <  1:1924775/69‑1 (MQ=255)
                              atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            <  1:1963237/69‑1 (MQ=255)
                              atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            <  1:957161/69‑1 (MQ=255)
                              atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            >  1:2497629/1‑69 (MQ=255)
                              atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            <  1:3196481/69‑1 (MQ=255)
                              atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            <  1:500719/69‑1 (MQ=255)
                               tCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGt                            <  1:1308985/68‑1 (MQ=255)
                                         tGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           >  1:250488/1‑43 (MQ=255)
                                         tGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           >  1:810954/1‑43 (MQ=255)
                                         tGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag                                           >  1:3071564/1‑43 (MQ=255)
                                           tCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGc               <  1:2135795/69‑1 (MQ=255)
                                           tCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGc               <  1:2497962/69‑1 (MQ=255)
                                            cGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCt              >  1:2161252/1‑69 (MQ=255)
                                            cGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCt              >  1:2437502/1‑69 (MQ=255)
                                            cGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCt              >  1:2025763/1‑69 (MQ=255)
                                            cGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCt              >  1:1203234/1‑69 (MQ=255)
                                             gTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGc               >  1:3311530/1‑67 (MQ=255)
                                             gTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtg             >  1:1663525/1‑69 (MQ=255)
                                             gTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtg             >  1:2687663/1‑69 (MQ=255)
                                             gTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtg             >  1:2618426/1‑69 (MQ=255)
                                             gTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtg             >  1:853619/1‑69 (MQ=255)
                                             gTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtg             >  1:1061356/1‑69 (MQ=255)
                                             gTTATCAGAAGCTT‑AACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtgt            <  1:374418/69‑1 (MQ=255)
                                               tATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtgt            <  1:1508864/68‑1 (MQ=255)
                                               tATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtgt            <  1:1183186/68‑1 (MQ=255)
                                               tATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtgt            <  1:2890779/68‑1 (MQ=255)
                                               tATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtgt            <  1:241560/68‑1 (MQ=255)
                                               tATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtgt            <  1:1453068/68‑1 (MQ=255)
                                               tATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtgt            <  1:2102371/68‑1 (MQ=255)
                                                aTCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCtgt            <  1:1927649/67‑1 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:831248/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:670183/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:553837/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:3325881/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:3284543/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:3283332/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:960358/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:1559749/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:2309835/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:150667/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaaca                     >  1:3155397/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGacaac                      >  1:936896/1‑52 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTCAGCTCCATCAGAATGTCATCTACAGTGacaaca                     >  1:1889363/1‑53 (MQ=255)
                                                     aaGCTTCCACCCATTTGGTAAGCTACATGAGAATGTCATCGTCAGTGccaac                      >  1:1385207/1‑52 (MQ=255)
                                                     aaGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCCGaa     >  1:1385202/1‑69 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:790981/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:1711031/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:73557/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:1013652/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:714350/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:909581/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:1496163/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:1060868/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:638551/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:339639/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:322278/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:3218034/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:2603404/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAg    <  1:1284248/69‑1 (MQ=255)
                                                      aGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTACTCTGCCCGAAg    <  1:1174461/69‑1 (MQ=255)
                                                      aGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGac                         >  1:1807025/1‑48 (MQ=255)
                                                      aGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGac                         >  1:2692701/1‑48 (MQ=255)
                                                        cTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCCGAAGGc  <  1:3435803/69‑1 (MQ=255)
                                                        cTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCCGAAGGc  <  1:2114382/69‑1 (MQ=255)
                                                        cTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCAGAAGGc  <  1:1267397/69‑1 (MQ=255)
                                                         ttCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCATTGACAACACCATGCTGTGCCCGAAGGc  <  1:2654210/68‑1 (MQ=255)
                                                            |                                                                
GACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCCGAAGGC  >  minE/941192‑941316

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