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 278,199 G→A 43.8% T304T (ACC→ACT)  cyoB ← cytochrome o ubiquinol oxidase subunit I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE278,1990GA43.8% 24.6 / 68.8 89T304T (ACC→ACT) cyoBcytochrome o ubiquinol oxidase subunit I
Reads supporting (aligned to +/- strand):  ref base G (32/18);  new base A (10/29);  total (42/47)
Fisher's exact test for biased strand distribution p-value = 5.40e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

GACAGCACGGTGATACAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGCAGGATCAGGATGTAAACTTCCGGGT  >  minE/278131‑278260
                                                                    |                                                             
gACAGCACGGTGATACAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAg                                                               <  1:3018271/69‑1 (MQ=255)
gACAGCACGGTGATACAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAg                                                               <  1:865883/69‑1 (MQ=255)
 aCAGCACGGTGATACAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAg                                                               <  1:2099207/68‑1 (MQ=255)
           gATACAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCaa                                                     >  1:1274050/1‑68 (MQ=255)
           gATACAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAAt                                                    >  1:2754205/1‑69 (MQ=255)
           gATACAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAAt                                                    >  1:272519/1‑69 (MQ=255)
              aCAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAAttt                                                  >  1:523123/1‑68 (MQ=255)
              aCAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAAttt                                                  >  1:507073/1‑68 (MQ=255)
                        gCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAacaca                                       <  1:1379343/69‑1 (MQ=255)
                        gCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAacaca                                       <  1:528774/69‑1 (MQ=255)
                        gCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAacaca                                       <  1:1678942/69‑1 (MQ=255)
                        gCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAacaca                                       <  1:2099453/69‑1 (MQ=255)
                        gCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAacaca                                       <  1:2828722/69‑1 (MQ=255)
                        gCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAacaca                                       <  1:1118028/69‑1 (MQ=255)
                               ccAGCGAGGTATAACCAAACAGCCGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGaa                                  >  1:2205481/1‑67 (MQ=255)
                               ccAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGaa                                  >  1:879773/1‑67 (MQ=255)
                               ccAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGaa                                  >  1:1668469/1‑67 (MQ=255)
                               ccAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGaa                                  >  1:2973340/1‑67 (MQ=255)
                               ccAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGaa                                  >  1:1904256/1‑67 (MQ=255)
                                cAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAc                               >  1:2385297/1‑69 (MQ=255)
                                cAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAc                               >  1:3376075/1‑69 (MQ=255)
                                cAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAc                               >  1:2314370/1‑69 (MQ=255)
                                cAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAc                               >  1:2262286/1‑69 (MQ=255)
                                cAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAc                               >  1:1208032/1‑69 (MQ=255)
                                cAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAc                               >  1:1166289/1‑69 (MQ=255)
                                       gTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAcaggcagg                        <  1:559651/69‑1 (MQ=255)
                                       gTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAcaggcagg                        <  1:648857/69‑1 (MQ=255)
                                       gTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAcaggcagg                        <  1:1353640/69‑1 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAca                              <  1:1687562/60‑1 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAca                              <  1:2027416/60‑1 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAca                              <  1:2065618/60‑1 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAca                              <  1:1655088/60‑1 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAca                              <  1:3320857/60‑1 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAca                              <  1:1040519/60‑1 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAca                              <  1:916273/60‑1 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:727378/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:3199077/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:1118027/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:2929877/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:117007/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:1303607/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:1571211/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:512504/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:760789/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatc                     >  1:853535/1‑69 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:2139375/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:1098369/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:3058169/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:687786/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:553276/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:2802471/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:154508/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:413822/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:477082/1‑67 (MQ=255)
                                          taACCAAACAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGcagga                       >  1:1329590/1‑67 (MQ=255)
                                           aaCCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAca                              <  1:2351565/59‑1 (MQ=255)
                                            aCCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatcag                   >  1:3229196/1‑69 (MQ=255)
                                            aCCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatcag                   >  1:996032/1‑69 (MQ=255)
                                            aCCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatcag                   >  1:784576/1‑69 (MQ=255)
                                            aCCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatcag                   >  1:1391014/1‑69 (MQ=255)
                                            aCCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGcaggatcag                   >  1:1905962/1‑69 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATAGAGGCAGGATCAAGATGTa             <  1:1417637/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:2985949/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1222153/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1248693/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1482094/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:795328/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1488099/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1532364/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1727783/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1944079/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1947021/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:2171688/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:242473/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:388163/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:299987/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:2915767/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:329545/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:3320478/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:263909/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:353481/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:392209/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:2586721/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:45413/69‑1 (MQ=255)
                                                  cAGACGTTTACGCGAGAAAGTTGCCGCAACTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTa             <  1:1957854/69‑1 (MQ=255)
                                                   aGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAAcaggcagg                        <  1:2222585/57‑1 (MQ=255)
                                                       gTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGCAGGATCAGGATGTAAACtt        >  1:1856277/1‑69 (MQ=255)
                                                              cgAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTAAACTTCCGGGt  <  1:244358/68‑1 (MQ=255)
                                                              cgAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTAAACTTCCGGGt  <  1:3391965/68‑1 (MQ=255)
                                                              cgAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTAAACTTCCGGGt  <  1:2795747/68‑1 (MQ=255)
                                                              cgAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTAAACTTCCGGGt  <  1:541417/68‑1 (MQ=255)
                                                              cgAGAAAGTTGCCGCAATTTCGGAGAACACACCGAATACAGGCAGGATCAAGATGTAAACTTCCGGGt  <  1:457929/68‑1 (MQ=255)
                                                                    |                                                             
GACAGCACGGTGATACAGACGGTTGCCCATACCAGCGAGGTATAACCAAACAGACGTTTACGCGAGAAGGTTGCCGCAATTTCGGAGAACACACCGAAAACAGGCAGGATCAGGATGTAAACTTCCGGGT  >  minE/278131‑278260

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