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 709,736 T→G 39.0% K47Q (AAA→CAA) ‡ yceJ ← predicted cytochrome b561

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE709,7360TG39.0% 36.4 / 77.9 82K47Q (AAA→CAA) ‡yceJpredicted cytochrome b561
Reads supporting (aligned to +/- strand):  ref base T (32/18);  new base G (17/15);  total (49/33)
Fisher's exact test for biased strand distribution p-value = 3.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

ACAGAACGCGAATAACCAGCCCCATCATTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCAAACATGC  >  minE/709670‑709795
                                                                  |                                                           
acaGAACGCGAATAACCAGCCCCATCATTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTtgt                                                           <  1:2285306/69‑1 (MQ=255)
acaGAACGCGAATAACCAGCCCCATCATTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTtgt                                                           <  1:1030779/69‑1 (MQ=255)
acaGAACGCGAATAACCAGCCCCATCATTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTtgt                                                           <  1:816344/69‑1 (MQ=255)
acaGAACGCGAATAACCAGCCCCATCATTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTtgt                                                           <  1:2378670/69‑1 (MQ=255)
 caGAACGCGAATAACCAGCCCCATCATTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTtgt                                                           <  1:1819313/68‑1 (MQ=255)
                  gCCCCATCATTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGtaat                                         <  1:1196304/69‑1 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:463198/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:2750907/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:3319247/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:2741406/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:1719508/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:1706109/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:1630809/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:1468987/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:773188/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:2746881/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:548756/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:478674/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:3092369/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:2510133/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:3282935/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:2526221/1‑69 (MQ=255)
                         catTAACAAAATGCCGATGCTTTTATGCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAg                                  >  1:1046340/1‑69 (MQ=255)
                         catTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAg                                  >  1:71006/1‑69 (MQ=255)
                         catTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAg                                  >  1:664401/1‑69 (MQ=255)
                          atTAAGAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGAt                                                        <  1:2579866/46‑1 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGAt                                                        <  1:701523/46‑1 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGAt                                                        <  1:3054913/46‑1 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGAt                                                        <  1:2041479/46‑1 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGAt                                                        <  1:1091215/46‑1 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAg                                  >  1:240178/1‑68 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:2594744/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:3278668/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:3431291/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:2562579/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:2546436/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:3404868/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:2021295/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:3377039/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:84406/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:1408269/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:1403006/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:856877/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:861962/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:1219499/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:1179868/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:1079706/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:895713/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGc                                 >  1:1038762/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTAATACCAGCCATCGTAATAACTGAGc                                 >  1:2639727/1‑69 (MQ=255)
                          atTAACAAAATACCGATGCTTTTATGCAATTCGGGTGCTTTGTGAt                                                        <  1:1213689/46‑1 (MQ=255)
                           ttAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGAt                                                        <  1:1834062/45‑1 (MQ=255)
                            tAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGt                               >  1:1967980/1‑69 (MQ=255)
                                aaaaTACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGAcc                           <  1:1240629/69‑1 (MQ=255)
                                     aCCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATc                        >  1:2309814/1‑67 (MQ=255)
                                     aCCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATc                        >  1:2059357/1‑67 (MQ=255)
                                     aCCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATc                        >  1:1805158/1‑67 (MQ=255)
                                     aCCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATc                        >  1:1632905/1‑67 (MQ=255)
                                     aCCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATc                        >  1:1218333/1‑67 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:642485/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:903245/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:3367415/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:1024086/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:2059286/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:145067/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:1440837/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:1427791/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:2022796/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:2994805/68‑1 (MQ=255)
                                                   gCAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:314388/68‑1 (MQ=255)
                                                    cAGTTCGTGTGCTTTTTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:1861105/69‑1 (MQ=255)
                                                    cAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:2793084/69‑1 (MQ=255)
                                                    cAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:2656240/69‑1 (MQ=255)
                                                    cAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:450826/69‑1 (MQ=255)
                                                    cAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:3372240/69‑1 (MQ=255)
                                                    cAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:1330601/69‑1 (MQ=255)
                                                    cAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:2948068/69‑1 (MQ=255)
                                                    cAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:162340/69‑1 (MQ=255)
                                                    cAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:1058954/67‑1 (MQ=255)
                                                    cAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:1028202/67‑1 (MQ=255)
                                                    cAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:1229512/67‑1 (MQ=255)
                                                    cAGTTCCGGTGCCTGGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCa         <  1:1528408/67‑1 (MQ=255)
                                                     aGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCaaa       <  1:1625108/68‑1 (MQ=255)
                                                         cGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCAAACATGc  >  1:1981627/1‑69 (MQ=255)
                                                         cGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCAAACATGc  >  1:482152/1‑69 (MQ=255)
                                                         cGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCAAACATGc  >  1:257251/1‑69 (MQ=255)
                                                         cGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCAAACATGc  >  1:3166045/1‑69 (MQ=255)
                                                                  |                                                           
ACAGAACGCGAATAACCAGCCCCATCATTAACAAAATACCGATGCTTTTATGCAGTTCGGGTGCTTTGTGATACCAGCCATCGTAATAACTGAGCGTGACCATCCACAGACCTAAAGCAAACATGC  >  minE/709670‑709795

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