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 2,122,416 T→C 31.2% A270A (GCA→GCG)  yraQ ← predicted permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,122,4160TC31.2% 99.6 / 56.1 112A270A (GCA→GCG) yraQpredicted permease
Reads supporting (aligned to +/- strand):  ref base T (30/47);  new base C (18/17);  total (48/64)
Fisher's exact test for biased strand distribution p-value = 2.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 118 total aligned reads displayed.

ATACCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCGGCATGGGGGAATAAC  >  minE/2122348‑2122482
                                                                    |                                                                  
aTACCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAATCATCCt                                                                    <  1:1363/69‑1 (MQ=255)
aTACCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCt                                                                    <  1:3106853/69‑1 (MQ=255)
aTACCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCt                                                                    <  1:3083111/69‑1 (MQ=255)
aTACCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCt                                                                    <  1:2622186/69‑1 (MQ=255)
  aCCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGc                                                                  >  1:56958/1‑69 (MQ=255)
  aCCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGc                                                                  <  1:2174916/69‑1 (MQ=255)
  aCCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGc                                                                  <  1:412928/69‑1 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACTGCCATCGcc                                                     >  1:1150231/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     <  1:1038530/69‑1 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     <  1:750232/69‑1 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     <  1:195204/69‑1 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:2136311/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:3334554/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:1796661/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:2412277/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:2579109/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:574079/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:1294602/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:3009969/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     <  1:463131/69‑1 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     >  1:2780865/1‑69 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGcc                                                     <  1:611409/69‑1 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      >  1:3093554/1‑68 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      >  1:2957746/1‑68 (MQ=255)
               atcGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCACCATCGcc                                                     <  1:122384/69‑1 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCt                                                                    >  1:2763110/1‑44 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      >  1:264006/1‑58 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      >  1:2229459/1‑58 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      >  1:3240667/1‑58 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      <  1:604643/58‑1 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      <  1:3251127/58‑1 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      <  1:1644401/58‑1 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      <  1:172393/58‑1 (MQ=255)
                         cAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGc                                                      >  1:1914011/1‑58 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:3341380/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:3215262/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:1170595/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:3354984/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:1252956/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:912963/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:3385343/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:3323209/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:666382/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:873822/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:2543385/68‑1 (MQ=255)
                           aTCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:620943/68‑1 (MQ=255)
                            tCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCt                                                                    <  1:1550875/41‑1 (MQ=255)
                                  tttCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGt                                  <  1:822766/69‑1 (MQ=255)
                                  tttCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGt                                  <  1:3429215/69‑1 (MQ=255)
                                  tttCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGt                                  <  1:182310/69‑1 (MQ=255)
                                   ttCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGt                                  <  1:2493742/68‑1 (MQ=255)
                                    tCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTa                                >  1:362001/1‑69 (MQ=255)
                                    tCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTa                                >  1:3016836/1‑69 (MQ=255)
                                    tCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTa                                >  1:2251975/1‑69 (MQ=255)
                                        ctgcCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATc                              <  1:2272454/67‑1 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           <  1:389159/68‑1 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           <  1:533741/68‑1 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           <  1:2818332/68‑1 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           <  1:875292/68‑1 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           <  1:1836762/68‑1 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           <  1:2224213/68‑1 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           <  1:2304622/68‑1 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGc                                                      >  1:457085/1‑41 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:2301442/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:2932536/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:127946/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:1450907/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:830832/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:1767257/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:1784437/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:1833016/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:277041/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:2004476/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:600944/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGAc                           >  1:2719621/1‑68 (MQ=255)
                                          gcCGTGGGAATGACAAACAAGCATCCCGCTACCGACATCGCCACCCCCCACATCAGGCTGTTATCGAc                           >  1:1273071/1‑68 (MQ=255)
                                               gggAATGACAAACAAGCATCCCGCTACCGCGATCGCCACCACCCACAt                                          <  1:2102044/48‑1 (MQ=38)
                                                   aTGACAAACAAGCATCCCGCTACCGCCATCGCCACCACCCACAt                                          <  1:1141656/44‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:870378/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:751531/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:693467/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:913168/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:2095507/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:1081125/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:1263820/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:1264452/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:1715737/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:2213729/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:2402053/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:2946369/69‑1 (MQ=255)
                                                    tGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:374266/69‑1 (MQ=255)
                                                     gACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:2562179/68‑1 (MQ=255)
                                                     gACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:2022649/68‑1 (MQ=255)
                                                     gACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:2813031/68‑1 (MQ=255)
                                                     gACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                <  1:1493340/68‑1 (MQ=255)
                                                      acaaacaaGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCgg                >  1:2073587/1‑67 (MQ=255)
                                                      acaaacaaGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCGGCa              >  1:1427742/1‑69 (MQ=255)
                                                                   cTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCGGCATGGGGGAATa    >  1:612380/1‑66 (MQ=255)
                                                                   cTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCGGCATGGGGGAATa    >  1:3312163/1‑66 (MQ=255)
                                                                   cTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCGGCATGGGGGAATAAc  >  1:498737/1‑68 (MQ=255)
                                                                    |                                                                  
ATACCTGCCAGCATCATCGTTTGTACAATCGGAATTTCTGCTGCCGTGGGAATGACAAACAAGCATCCTGCTACCGCCATCGCCACCACCCACATCAGGCTGTTATCGACAGCACCATCGGCATGGGGGAATAAC  >  minE/2122348‑2122482

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