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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,321,783 G→A 78.7% intergenic (‑237/+257) gnd ← / ← galF gluconate‑6‑phosphate dehydrogenase, decarboxylating/predicted subunit with GalU

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,321,7830GA78.7% 165.9 / 41.9 89intergenic (‑237/+257)gnd/galFgluconate‑6‑phosphate dehydrogenase, decarboxylating/predicted subunit with GalU
Reads supporting (aligned to +/- strand):  ref base G (12/7);  new base A (32/38);  total (44/45)
Fisher's exact test for biased strand distribution p-value = 2.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.07e-01

AGTTTGATTAATAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTAATT  >  minE/1321718‑1321848
                                                                 |                                                                 
aGTTTGATTAATAGAGGTATTAATGCACGCTTCCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATg                                                                 <  1:52593/68‑1 (MQ=255)
aGTTTGATTAATAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTgcatgcat                                                              >  1:3445905/1‑71 (MQ=255)
aGTTTGATTAATAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTg                                                                 <  1:3338360/68‑1 (MQ=255)
aGTTTGATTAATAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCAt                                                              >  1:2579334/1‑71 (MQ=255)
aGTTTGATTAATAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATg                                                                 <  1:891619/68‑1 (MQ=255)
  tttGATTAATAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCatgcatgc                                                            >  1:3940797/1‑71 (MQ=255)
         aaTAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTatga                                                      <  1:1760185/70‑1 (MQ=255)
           tAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGAtgt                                                   <  1:5252776/71‑1 (MQ=255)
           tAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGAtgt                                                   >  1:3879490/1‑71 (MQ=255)
               ggTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGAtgt                                                   <  1:1278969/67‑1 (MQ=255)
               ggTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGAtgt                                                   <  1:4212536/67‑1 (MQ=255)
                 tATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGa                                                 >  1:2005607/1‑67 (MQ=255)
                   ttAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGa                                                 >  1:564217/1‑65 (MQ=255)
                   ttAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGc                                            <  1:1662753/70‑1 (MQ=255)
                     aaTGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGt                                          >  1:1074575/1‑70 (MQ=255)
                     aaTGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGt                                          >  1:3859690/1‑70 (MQ=255)
                      aTGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGtt                                         <  1:5506644/70‑1 (MQ=255)
                      aTGCACGCTACCGCCCCTGGCCTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGtt                                         <  1:5513184/70‑1 (MQ=39)
                       tGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTAc                                       >  1:2426526/1‑71 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTAcc                                      >  1:2672634/1‑70 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTAcc                                      >  1:2031302/1‑70 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTAcc                                      >  1:4368028/1‑70 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTAcc                                      >  1:1551525/1‑70 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTAcc                                      >  1:1325365/1‑70 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTAcc                                      >  1:2010147/1‑70 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTAcc                                      >  1:4473276/1‑70 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTAcc                                      >  1:3368876/1‑70 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTAcc                                      <  1:3589473/70‑1 (MQ=255)
                         cACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTAc                                       >  1:4929131/1‑69 (MQ=255)
                             cTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTc                                 >  1:3350964/1‑71 (MQ=255)
                             cTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTc                                 >  1:5598671/1‑71 (MQ=255)
                              tACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTACCCACTcg                                >  1:3041943/1‑71 (MQ=255)
                                ccGCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTcg                                <  1:3779996/69‑1 (MQ=255)
                                  gCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGa                                                 >  1:3161818/1‑50 (MQ=255)
                                  gCCCCTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCt                            <  1:2406563/71‑1 (MQ=255)
                                   ccccTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTa                           <  1:2021323/71‑1 (MQ=255)
                                     ccTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTaaa                         <  1:5475878/71‑1 (MQ=255)
                                     ccTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTaaa                         >  1:636023/1‑71 (MQ=255)
                                     ccTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTaaa                         >  1:2729895/1‑71 (MQ=255)
                                      cTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTatga                                                      >  1:5110812/1‑41 (MQ=255)
                                      cTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGAtgt                                                   <  1:1337513/44‑1 (MQ=255)
                                      cTGGCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGtt                                         <  1:4946898/54‑1 (MQ=255)
                                       tGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTa                           <  1:1467784/67‑1 (MQ=255)
                                       tGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTa                           <  1:1893568/67‑1 (MQ=255)
                                        ggCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAAccc                      >  1:4417312/1‑71 (MQ=255)
                                        ggCTTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAAccc                      >  1:3970317/1‑71 (MQ=255)
                                            ttACAGCTACCAGAGCTCTGCATGCATGCCTATGATGTGACGAGCg                                           <  1:1274676/46‑1 (MQ=255)
                                            ttACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCg                                           <  1:2144387/46‑1 (MQ=255)
                                             tACAGCTACCAGAGCACTGCATGCATGCCTATGAtgtg                                                  <  1:3212394/38‑1 (MQ=255)
                                             tACAGCTACCAGAGCACTGCATGCATGCCTATGAtgtg                                                  <  1:2233376/38‑1 (MQ=255)
                                             tACAGCTACCAGAGCACTGCATGCATGCCTATGAtgtg                                                  <  1:5010995/38‑1 (MQ=255)
                                             tACAGCTACCAGAGCACTGCATGCATGCCTATGAtgtg                                                  <  1:2563939/38‑1 (MQ=255)
                                             tACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTaaa                         >  1:138449/1‑63 (MQ=255)
                                             tACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTaaa                         >  1:3510441/1‑63 (MQ=255)
                                             tACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTaaa                         >  1:302463/1‑63 (MQ=255)
                                             tACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTaaa                         >  1:3568176/1‑63 (MQ=255)
                                              aCAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGtt                                         >  1:2882312/1‑46 (MQ=255)
                                              aCAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGtt                                         >  1:325971/1‑46 (MQ=255)
                                              aCAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGt                                          >  1:2803968/1‑45 (MQ=255)
                                                   tACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACt                                  >  1:3510649/1‑48 (MQ=255)
                                                   tACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACt                                  >  1:3222881/1‑48 (MQ=255)
                                                   tACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACt                                  >  1:5614923/1‑48 (MQ=255)
                                                   tACCAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCa            >  1:1742064/1‑70 (MQ=255)
                                                    aCCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCg                                           >  1:2586330/1‑38 (MQ=255)
                                                      cAGAGCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACg        <  1:158425/71‑1 (MQ=255)
                                                       agagCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGaaaaa                <  1:4074554/62‑1 (MQ=255)
                                                       agagCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGc       >  1:5118264/1‑71 (MQ=255)
                                                        gagCACTGCGTGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGc       >  1:5049572/1‑70 (MQ=255)
                                                         agCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTaa                          <  1:5546359/50‑1 (MQ=255)
                                                         agCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTa     <  1:3428785/71‑1 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTa                           <  1:1633315/48‑1 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAAt               <  1:781138/60‑1 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAAt               <  1:4200544/60‑1 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAAt               <  1:2658765/60‑1 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTaa    >  1:2239573/1‑71 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTaa    >  1:4811324/1‑71 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTaa    <  1:2864461/71‑1 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTaa    >  1:2450649/1‑71 (MQ=255)
                                                          gCACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTaa    <  1:879341/71‑1 (MQ=255)
                                                           cACTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTa     >  1:5538892/1‑69 (MQ=255)
                                                            aCTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAAtt              <  1:453979/59‑1 (MQ=255)
                                                            aCTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTAAtt  <  1:3676496/71‑1 (MQ=255)
                                                            aCTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTAAtt  <  1:3936584/71‑1 (MQ=255)
                                                            aCTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTAAtt  <  1:1546382/71‑1 (MQ=255)
                                                             cTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGaaaa                 <  1:5321842/55‑1 (MQ=255)
                                                             cTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGaaaa                 <  1:4395558/55‑1 (MQ=255)
                                                             cTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGaaaa                 <  1:3067283/55‑1 (MQ=255)
                                                             cTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGaaaa                 <  1:2502015/55‑1 (MQ=255)
                                                             cTGCATGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGaaaa                 <  1:851880/55‑1 (MQ=255)
                                                             cTGCATGCATGCCTATGATGTGACGAGCGTTACCCAATCGCGCTAAACCCGAAAAATTCAAACGCTAAtt  <  1:1822620/70‑1 (MQ=255)
                                                              tgcatgcaTGCCTATGATGTGACGAGCGTTACCCACTCGCGCt                            <  1:5217284/43‑1 (MQ=255)
                                                              tgcatgcaTGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCa            >  1:5417407/1‑59 (MQ=255)
                                                              tgcatgcaTGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCt      <  1:1892847/65‑1 (MQ=255)
                                                              tgcatgcaTGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCt      <  1:3170265/65‑1 (MQ=255)
                                                              tgcatgcaTGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCt      <  1:576250/65‑1 (MQ=255)
                                                              tgcatgcaTGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCt      <  1:2138216/65‑1 (MQ=255)
                                                               gCGTGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCaaa          >  1:102883/1‑60 (MQ=255)
                                                                 |                                                                 
AGTTTGATTAATAGAGGTATTAATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCGTGCATGCCTATGATGTGACGAGCGTTACCCACTCGCGCTAAACCCGAAAAATTCAAACGCTAATT  >  minE/1321718‑1321848

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A