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 615,035 T→C 36.0% Y228Y (TAT→TAC)  serC → 3‑phosphoserine/phosphohydroxythreonine aminotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE615,0350TC36.0% 86.3 / 85.1 136Y228Y (TAT→TAC) serC3‑phosphoserine/phosphohydroxythreonine aminotransferase
Reads supporting (aligned to +/- strand):  ref base T (38/49);  new base C (28/21);  total (66/70)
Fisher's exact test for biased strand distribution p-value = 1.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

Only 100 of 144 total aligned reads displayed.

ACAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCT  >  minE/614967‑615094
                                                                    |                                                           
aCAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGattat                                                             >  1:1827932/1‑69 (MQ=255)
aCAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGattat                                                             >  1:2652800/1‑69 (MQ=255)
aCAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGattat                                                             >  1:685623/1‑69 (MQ=255)
aCAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGattat                                                             >  1:1525293/1‑69 (MQ=255)
aCAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGattat                                                             >  1:569072/1‑69 (MQ=255)
aCAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGattat                                                             >  1:1389095/1‑69 (MQ=255)
aCAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGattat                                                             >  1:2370886/1‑69 (MQ=255)
     cGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTcc                                                          >  1:2329379/1‑67 (MQ=255)
     cGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTcc                                                          >  1:348931/1‑67 (MQ=255)
     cGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTcc                                                          >  1:3350628/1‑67 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:841809/65‑1 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:1191846/65‑1 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:119007/65‑1 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:2130678/65‑1 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:545217/65‑1 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:40449/65‑1 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:1813588/65‑1 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:2921287/65‑1 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCAt                                                        >  1:2131587/1‑68 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATc                                                       >  1:2402844/1‑69 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATc                                                       >  1:2018112/1‑69 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATc                                                       >  1:587677/1‑69 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATc                                                       >  1:2957107/1‑69 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATc                                                       >  1:1955525/1‑69 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATc                                                       >  1:865445/1‑69 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATc                                                       >  1:1771004/1‑69 (MQ=255)
      gTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATc                                                       >  1:1868318/1‑69 (MQ=255)
       tCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:2758935/64‑1 (MQ=255)
                         tGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCa                                    >  1:1016786/1‑69 (MQ=255)
                         tGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCa                                    >  1:2320464/1‑69 (MQ=255)
                            tGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATg                                  <  1:2495653/68‑1 (MQ=255)
                            tGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATg                                  <  1:2012771/68‑1 (MQ=255)
                            tGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATg                                  <  1:1403376/68‑1 (MQ=255)
                            tGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATg                                  <  1:1704575/68‑1 (MQ=255)
                               gCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTc                                                           <  1:385919/40‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                               <  1:2266509/67‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                               <  1:3315192/67‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                               <  1:1436857/67‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                               <  1:2136304/67‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                               <  1:1662265/67‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                             <  1:595993/69‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                             <  1:3074302/69‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                             <  1:2531606/69‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                             <  1:77056/69‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                             <  1:1128620/69‑1 (MQ=255)
                                cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                             <  1:599385/69‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:1738739/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:698796/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:1929735/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:2770392/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:1804135/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:2251158/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:1531487/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:434736/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:2191608/62‑1 (MQ=255)
                                 aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACAATAACGATTCCAt                                   <  1:2996315/62‑1 (MQ=255)
                                  aaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:548238/61‑1 (MQ=255)
                                   aGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAacac                          <  1:272812/69‑1 (MQ=255)
                                   aGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAacac                          <  1:863835/69‑1 (MQ=255)
                                             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGCCa                <  1:1461563/69‑1 (MQ=255)
                                             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                <  1:2974625/69‑1 (MQ=255)
                                             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                <  1:3186298/69‑1 (MQ=255)
                                             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                <  1:615599/69‑1 (MQ=255)
                                             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                <  1:1992178/69‑1 (MQ=255)
                                             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                <  1:1901405/69‑1 (MQ=255)
                                             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                <  1:975698/69‑1 (MQ=255)
                                                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc          >  1:755896/1‑69 (MQ=255)
                                                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc          >  1:3381704/1‑69 (MQ=255)
                                                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc          >  1:1552367/1‑69 (MQ=255)
                                                    cGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCt         <  1:1057227/69‑1 (MQ=255)
                                                        gATTCTGGTTTACTCCATCCTCAACGATAACGATTCCAt                                   <  1:2472758/39‑1 (MQ=25)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:316965/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:967627/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:1088381/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:1269048/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:1389405/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:1776450/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:71841/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:693954/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2082691/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2159136/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:217016/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2202095/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2412733/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:3022708/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2962818/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2812168/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2638824/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2530137/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2483330/1‑46 (MQ=255)
                                                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                            >  1:2351231/1‑46 (MQ=255)
                                                           tCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGtatct  <  1:2066864/69‑1 (MQ=255)
                                                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                 >  1:642930/1‑53 (MQ=255)
                                                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                 >  1:1986862/1‑53 (MQ=255)
                                                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                 >  1:757916/1‑53 (MQ=255)
                                                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                 >  1:47696/1‑53 (MQ=255)
                                                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                 >  1:3064436/1‑53 (MQ=255)
                                                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                 >  1:1032027/1‑53 (MQ=255)
                                                            cTGGATTATTCCATCCTCAACGATAACGGCTCAATGTTTAACACGCCGCCGAc                 >  1:3284511/1‑53 (MQ=255)
                                                              ggATTATTCCATCCTCAACGATAACGTCTCCATGttt                               <  1:2047288/37‑1 (MQ=255)
                                                                    |                                                           
ACAATCGTCATCGTTCGTGAAGATTTGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCT  >  minE/614967‑615094

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