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 451,488 C→T 21.8% A182A (GCG→GCA)  kdpA ← potassium translocating ATPase, subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE451,4880CT21.8% 143.2 / 28.1 100A182A (GCG→GCA) kdpApotassium translocating ATPase, subunit A
Reads supporting (aligned to +/- strand):  ref base C (35/43);  new base T (13/9);  total (48/52)
Fisher's exact test for biased strand distribution p-value = 3.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.68e-01

Only 100 of 108 total aligned reads displayed.

CACAGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCT  >  minE/451422‑451553
                                                                  |                                                                 
cacaGCCTGATAAGGCAGAAAGTTTTGCAGCGCTCCTTGTTGAATAAAAAACAGTGCAATCAACAACGc                                                                 >  1:869987/1‑69 (MQ=255)
cacaGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGc                                                                 >  1:282951/1‑69 (MQ=255)
cacaGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGc                                                                 >  1:2913638/1‑69 (MQ=255)
cacaGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGc                                                                 >  1:2506091/1‑69 (MQ=255)
  caGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGcc                                                                <  1:1124503/68‑1 (MQ=255)
  caGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGcc                                                                <  1:1163220/68‑1 (MQ=255)
  caGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGcc                                                                <  1:1553304/68‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:1006089/69‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:1958649/69‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:194349/69‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:2779591/69‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:2927979/69‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:2954039/69‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:1543022/69‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:3264815/69‑1 (MQ=255)
      cTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:2192352/69‑1 (MQ=255)
       tGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAggg                                                          <  1:710893/69‑1 (MQ=255)
       tGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAggg                                                          <  1:3102529/69‑1 (MQ=255)
       tGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAggg                                                          <  1:1658180/69‑1 (MQ=255)
       tGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAggg                                                          <  1:2132061/69‑1 (MQ=255)
        gATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAggg                                                          <  1:1214799/68‑1 (MQ=255)
           aaGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGTCt                                                       >  1:2429/1‑68 (MQ=255)
           aaGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACt                                                       >  1:3025430/1‑68 (MQ=255)
           aaGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACt                                                       <  1:2176875/68‑1 (MQ=255)
           aaGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACt                                                       <  1:2580740/68‑1 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           <  1:1243494/61‑1 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg                                                     <  1:3046805/67‑1 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg                                                     <  1:2846916/67‑1 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg                                                     <  1:2882688/67‑1 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg                                                     <  1:2479046/67‑1 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa                                                   >  1:602376/1‑69 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa                                                   >  1:1682277/1‑69 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa                                                   >  1:2636659/1‑69 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa                                                   >  1:2059857/1‑69 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa                                                   >  1:1982245/1‑69 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa                                                   >  1:774006/1‑69 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa                                                   >  1:152871/1‑69 (MQ=255)
              gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa                                                   >  1:418051/1‑69 (MQ=255)
               cAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAgg                                                           >  1:2584942/1‑60 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:577268/69‑1 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:218266/69‑1 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:571336/69‑1 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:3301808/69‑1 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:4566/69‑1 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:2393143/69‑1 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:2374971/69‑1 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:1102223/69‑1 (MQ=255)
                     gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa                                            <  1:719768/69‑1 (MQ=255)
                        ttGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGcc                                                                <  1:688241/46‑1 (MQ=255)
                                   cTTGTTGAATAAAATACAGTGCAATCAACAACGCCACAggg                                                          <  1:1554421/41‑1 (MQ=255)
                                    ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg                                                     <  1:1739659/45‑1 (MQ=255)
                                    ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:656512/69‑1 (MQ=255)
                                    ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:744943/69‑1 (MQ=255)
                                    ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:2966468/69‑1 (MQ=255)
                                    ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:1576099/69‑1 (MQ=255)
                                    ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:2565175/69‑1 (MQ=255)
                                    ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:1191916/69‑1 (MQ=255)
                                    ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:633449/69‑1 (MQ=255)
                                                   cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:623687/54‑1 (MQ=255)
                                                   cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:3275991/54‑1 (MQ=255)
                                                   cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:1216571/54‑1 (MQ=255)
                                                   cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:1668383/54‑1 (MQ=255)
                                                   cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:2221332/54‑1 (MQ=255)
                                                   cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:2748974/54‑1 (MQ=255)
                                                   cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:649172/54‑1 (MQ=255)
                                                   cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg                             <  1:2107227/54‑1 (MQ=255)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:469492/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:1718880/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:401818/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:474377/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:5295/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:539216/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:1283635/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:833154/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:810623/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:2763259/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:1853756/3‑44 (MQ=37)
                                                        cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt                                  >  1:1615103/3‑44 (MQ=37)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:1012912/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:1290962/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:1309414/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:1334428/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:3029395/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:161906/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:1839605/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:2329595/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:2004867/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGt                                         >  1:2093905/1‑37 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCg                         >  1:3311202/1‑53 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa         >  1:2117784/1‑69 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa         >  1:2184529/1‑69 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa         >  1:1839305/1‑69 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa         >  1:268060/1‑69 (MQ=255)
                                                        cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa         >  1:3286042/1‑69 (MQ=255)
                                                               caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt  <  1:2077977/69‑1 (MQ=255)
                                                               caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt  <  1:241636/69‑1 (MQ=255)
                                                               caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt  <  1:756283/69‑1 (MQ=255)
                                                               caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt  <  1:3404993/69‑1 (MQ=255)
                                                               caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt  <  1:896898/69‑1 (MQ=255)
                                                                aacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt  <  1:571078/68‑1 (MQ=255)
                                                                  |                                                                 
CACAGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCT  >  minE/451422‑451553

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