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 2,700,542 G→T 36.3% V50V (GTG→GTT)  hofQ → predicted fimbrial transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,700,5420GT36.3% 97.5 / 72.4 99V50V (GTG→GTT) hofQpredicted fimbrial transporter
Reads supporting (aligned to +/- strand):  ref base G (22/41);  new base T (19/17);  total (41/58)
Fisher's exact test for biased strand distribution p-value = 9.39e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 104 total aligned reads displayed.

GTGGATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAGGCA  >  minE/2700474‑2700602
                                                                    |                                                            
gtggATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCgtg                                                              >  1:1581325/1‑69 (MQ=255)
gtggATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCgtg                                                              >  1:800296/1‑69 (MQ=255)
gtggATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCgtg                                                              >  1:2075862/1‑69 (MQ=255)
gtggATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCgtg                                                              >  1:2338609/1‑69 (MQ=255)
   gATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCgtgt                                                             >  1:661302/1‑67 (MQ=255)
   gATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTc                                                            >  1:181783/1‑68 (MQ=255)
   gATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTc                                                            >  1:1116721/1‑68 (MQ=255)
   gATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTc                                                            >  1:751791/1‑68 (MQ=255)
   gATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTc                                                            >  1:3148233/1‑68 (MQ=255)
   gATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTc                                                            >  1:1394174/1‑68 (MQ=255)
               gTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGc                                               <  1:3017769/69‑1 (MQ=255)
               gTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGc                                               <  1:184808/69‑1 (MQ=255)
               gTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGc                                               <  1:216719/69‑1 (MQ=255)
               gTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGc                                               <  1:1389453/69‑1 (MQ=255)
               gTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGc                                               <  1:1354563/69‑1 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:2226018/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:2590092/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:2701681/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:1873581/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:2936068/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:2998453/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:49840/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:348771/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:414068/1‑69 (MQ=255)
                  gCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGt                                            >  1:43537/1‑69 (MQ=255)
                           ttGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTc                                    >  1:3148594/1‑68 (MQ=255)
                             gCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGt                                  >  1:3262668/1‑68 (MQ=255)
                             gCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGt                                  <  1:34774/68‑1 (MQ=255)
                             gCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGt                                  <  1:2232600/68‑1 (MQ=255)
                             gCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGt                                  <  1:643579/68‑1 (MQ=255)
                             gCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGt                                  >  1:1502284/1‑68 (MQ=255)
                             gCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGt                                  <  1:2028663/68‑1 (MQ=255)
                             gCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGt                                  <  1:2736144/68‑1 (MQ=255)
                                ggCGCTGTCTGAACAGGAGAAGTTGTACCTGGTGGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACa                              <  1:1236247/69‑1 (MQ=255)
                                ggCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGc                                               <  1:2044889/52‑1 (MQ=255)
                                ggCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACa                              <  1:2195478/69‑1 (MQ=255)
                                 gcgcTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACa                              >  1:567479/1‑68 (MQ=255)
                                 gcgcTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACa                              <  1:1694192/68‑1 (MQ=255)
                                 gcgcTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACa                              >  1:727749/1‑68 (MQ=255)
                                    ctggctgTACAGGAGAAGTTGAACCTGGTGGTTTCTCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:1462260/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCtt                          <  1:687063/69‑2 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:461918/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:2257079/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:3123150/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:1448653/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:2585429/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:3028124/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:1117871/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:3287793/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:1810503/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:1481256/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:2056926/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:2036755/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:1990907/69‑1 (MQ=255)
                                    ctggctgAACAGGAGAAGTTGAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTa                          <  1:70620/69‑1 (MQ=255)
                                         tgAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAg                      <  1:1459728/68‑1 (MQ=255)
                                         tgAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAg                      <  1:486571/68‑1 (MQ=255)
                                         tgAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAg                      <  1:351972/68‑1 (MQ=255)
                                         tgAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAg                      <  1:691625/68‑1 (MQ=255)
                                         tgAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAg                      <  1:682124/68‑1 (MQ=255)
                                         tgAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAg                      <  1:2555266/68‑1 (MQ=255)
                                         tgAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAg                      <  1:234332/68‑1 (MQ=255)
                                                       tGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGc       <  1:2759917/69‑1 (MQ=255)
                                                        gacccTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:2147635/4‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCTGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:2805425/1‑69 (MQ=39)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:37902/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:532306/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:2831157/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1037605/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1104873/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1177438/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1469077/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1533611/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1601408/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1620560/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1776635/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:1799082/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:2265090/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:2343607/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:2731110/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:2850838/1‑69 (MQ=255)
                                                        gAACCTGGTGGTTTCGCCAGACGTCAGCAGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCa      >  1:541159/1‑69 (MQ=39)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:565917/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:847762/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:935553/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:3271684/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:2619405/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:1563254/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:152242/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:1447711/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAgg    <  1:1069751/68‑1 (MQ=255)
                                                           ccTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCAGGAAGCAgg    <  1:706540/68‑1 (MQ=255)
                                                            cTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAGGCa  <  1:1881341/69‑1 (MQ=255)
                                                            cTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAGGCa  <  1:1865297/69‑1 (MQ=255)
                                                             tGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTa                                <  1:3224816/38‑1 (MQ=255)
                                                             tGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTa                                <  1:2905766/38‑1 (MQ=255)
                                                             tGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTa                                <  1:2901509/38‑1 (MQ=255)
                                                             tGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTa                                <  1:2750204/38‑1 (MQ=255)
                                                             tGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTa                                <  1:230863/38‑1 (MQ=255)
                                                             tGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTa                                <  1:1660376/38‑1 (MQ=255)
                                                                    |                                                            
GTGGATGACGTTCCGGTAGCTCAGGTGTTGCAGGCGCTGGCTGAACAGGAGAAGTTGAACCTGGTCGTGTCGCCAGACGTCAGCGGTACGGTGTCGTTACATCTAACAGATGTTCCCTGGAAGCAGGCA  >  minE/2700474‑2700602

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