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 2,092,496 A→G 31.0% S218S (AGT→AGC)  yhaO ← predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,092,4960AG31.0% 75.5 / 42.2 88S218S (AGT→AGC) yhaOpredicted transporter
Reads supporting (aligned to +/- strand):  ref base A (38/22);  new base G (11/16);  total (49/39)
Fisher's exact test for biased strand distribution p-value = 6.31e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

GCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGTTTTTCACC  >  minE/2092428‑2092562
                                                                    |                                                                  
gCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGa                                                                    <  1:3434967/69‑1 (MQ=255)
gCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGa                                                                    <  1:3315763/69‑1 (MQ=255)
gCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGa                                                                    <  1:261630/69‑1 (MQ=255)
gCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGa                                                                    <  1:2764000/69‑1 (MQ=255)
gCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGa                                                                    <  1:671568/69‑1 (MQ=255)
gCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGa                                                                    <  1:2942176/69‑1 (MQ=255)
gCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGa                                                                    <  1:2212164/69‑1 (MQ=255)
gCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGa                                                                    <  1:2216216/69‑1 (MQ=255)
   cGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACtt                                                                 <  1:234832/69‑1 (MQ=255)
   cGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACtt                                                                 <  1:69663/69‑1 (MQ=255)
   cGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACtt                                                                 <  1:1381929/69‑1 (MQ=255)
            ttATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTg                                                         <  1:1131106/68‑1 (MQ=255)
                gCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:2400076/1‑68 (MQ=255)
                gCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:1937341/1‑68 (MQ=255)
                gCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:1299382/1‑68 (MQ=255)
                 ccGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:1356938/1‑67 (MQ=255)
                 ccGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:2791532/1‑67 (MQ=255)
                 ccGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:469335/1‑67 (MQ=255)
                 ccGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:365676/1‑67 (MQ=255)
                 ccGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:527276/1‑67 (MQ=255)
                 ccGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:916804/1‑67 (MQ=255)
                 ccGCGCCACTTCAATTGAGTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:2520478/1‑67 (MQ=255)
                  cgcgCCACTTCAATTGATTTTTCCCTCGAGAGATAAGAGATCACCATCGGACTTAACGTCTGGATa                                                     >  1:3062310/1‑66 (MQ=255)
                        aCTTCAATTGATTTTTTCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:2257271/69‑1 (MQ=255)
                        aCTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:1102794/69‑1 (MQ=255)
                        aCTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:2357478/69‑1 (MQ=255)
                        aCTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:402940/69‑1 (MQ=255)
                        aCTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:699687/69‑1 (MQ=255)
                        aCTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:2076803/69‑1 (MQ=255)
                        aCTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:2073895/69‑1 (MQ=255)
                        aCTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:2374962/69‑1 (MQ=255)
                        aCTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATc                                            <  1:1897461/69‑1 (MQ=255)
                           tCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGa                                          >  1:1581713/1‑68 (MQ=255)
                           tCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGAc                                         >  1:1532713/1‑69 (MQ=255)
                           tCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATAGAc                                         >  1:3024878/1‑69 (MQ=255)
                           tCAATTGATTATTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGa                                          >  1:2170904/1‑68 (MQ=255)
                            cAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGAc                                         >  1:3162581/1‑68 (MQ=255)
                                tGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAg                                    >  1:3426418/1‑69 (MQ=255)
                                tGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAg                                    >  1:2209009/1‑69 (MQ=255)
                                tGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAg                                    >  1:1348382/1‑69 (MQ=255)
                                    ttttCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTa                                <  1:1559624/69‑1 (MQ=255)
                                         ccGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAAc                             >  1:2007409/1‑67 (MQ=255)
                                         ccGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAAc                             >  1:750974/1‑67 (MQ=255)
                                         ccGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAAc                             >  1:1725374/1‑67 (MQ=255)
                                         ccGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAAc                             >  1:1288561/1‑67 (MQ=255)
                                               gcgaTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCATGGTAAACGGCAGCGt                     <  1:1824083/69‑1 (MQ=255)
                                               gcgaTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGt                     <  1:1688867/69‑1 (MQ=255)
                                               gcgaTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGt                     <  1:2154806/69‑1 (MQ=255)
                                                cgaTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGt                     >  1:1401096/1‑68 (MQ=255)
                                                agaTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACg                                        >  1:1054042/2‑49 (MQ=255)
                                                  aTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGtaat                  <  1:312524/69‑1 (MQ=255)
                                                  aTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGtaat                  <  1:318126/69‑1 (MQ=255)
                                                  aTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGtaat                  <  1:1076157/69‑1 (MQ=255)
                                                  aTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGtaat                  <  1:1793729/69‑1 (MQ=255)
                                                  aTAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGtaat                  <  1:2028274/69‑1 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:937350/1‑69 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:1463956/1‑69 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:1513664/1‑69 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:3277082/1‑69 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:3252341/1‑69 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:1109284/1‑69 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:724424/1‑69 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:2250694/1‑69 (MQ=255)
                                                          tCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGt          >  1:2634447/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGtaat                  >  1:2383391/1‑60 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:422708/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:1202175/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:1160305/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:2566127/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:1661828/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:58900/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:629085/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:928525/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:2367351/1‑69 (MQ=255)
                                                           cACCATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGtt         >  1:2138273/1‑69 (MQ=255)
                                                              cATCGGTCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAATCGGCATCGTAATAATGGCGttttt      <  1:2978705/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:1157435/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:1091976/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:1088248/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:1084581/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:89909/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:1778632/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:413650/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:380938/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:379520/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:2509950/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:338816/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:1860002/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:1977731/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:3080165/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:257340/69‑1 (MQ=255)
                                                              cATCGGGCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGttttt      <  1:2477681/69‑1 (MQ=255)
                                                                  ggACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGTTTTTCAcc  >  1:3165397/1‑69 (MQ=255)
                                                                  ggACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGTTTTTCAcc  >  1:883493/1‑69 (MQ=255)
                                                                  ggACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGTTTTTCAcc  >  1:2992878/1‑69 (MQ=255)
                                                                  ggACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGTTTTTCAcc  >  1:2180690/1‑69 (MQ=255)
                                                                    aCTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGTTTTTCAcc  >  1:1867943/1‑67 (MQ=255)
                                                                    aCTTAACGTCTGGAAAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGTTTTTCAcc  >  1:928272/1‑67 (MQ=255)
                                                                    |                                                                  
GCCCGCAATGCTTTATGCCGCGCCACTTCAATTGATTTTTCCCGCGAGCGATAAGAGATCACCATCGGACTTAACGTCTGGATAAACAGAATCGACGTCAGGGTAAACGGCAGCGTAATAATGGCGTTTTTCACC  >  minE/2092428‑2092562

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