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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,983,818 A→G 33.6% V144A (GTG→GCG)  yqeF ← predicted acyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,983,8180AG33.6% 129.1 / 109.5 113V144A (GTG→GCG) yqeFpredicted acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (41/34);  new base G (24/14);  total (65/48)
Fisher's exact test for biased strand distribution p-value = 4.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.18e-01

Only 100 of 116 total aligned reads displayed.

TTCGCGAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACATGTG  >  W3110S.gb/2983748‑2983884
                                                                      |                                                                  
ttCGCGAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGca                                                                    >  1:2907078/1‑71 (MQ=255)
   gcgAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACaa                                                                 <  1:3117661/71‑1 (MQ=255)
      aGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGAc                                                              <  1:2682141/71‑1 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTc                                                          <  1:479040/71‑1 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGAc                                                              >  1:1637454/1‑67 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGt                                                           >  1:165983/1‑70 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGt                                                           >  1:1363698/1‑70 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:2262017/71‑1 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:2722201/71‑1 (MQ=255)
           gATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCA‑AAGACTGTc                                                          <  1:2284452/69‑1 (MQ=255)
             ttttCGGCGGTGACGCCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaac                                                       >  1:3797908/1‑71 (MQ=255)
             ttttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaac                                                       >  1:2994413/1‑71 (MQ=255)
             ttttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaac                                                       >  1:119355/1‑71 (MQ=255)
              tttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaac                                                       >  1:1260458/1‑70 (MQ=255)
              tttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaac                                                       >  1:1477966/1‑70 (MQ=255)
              tttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaac                                                       >  1:750677/1‑70 (MQ=255)
                     ggTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGc                                               <  1:189585/71‑1 (MQ=255)
                        gACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                            >  1:4063354/1‑71 (MQ=255)
                        gACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                            >  1:3349506/1‑71 (MQ=255)
                         acacCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAtt                                           >  1:2373367/1‑71 (MQ=255)
                          cacCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCt                                              <  1:3555991/67‑1 (MQ=255)
                           acCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaaccaa                                                    >  1:1206287/1‑60 (MQ=255)
                             cAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaaccaac                                                   >  1:1121281/1‑59 (MQ=255)
                              aaTATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGa                                                               >  1:2784905/1‑46 (MQ=255)
                              aaTATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:3323871/51‑1 (MQ=255)
                               atatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAg                                                                <  1:2846523/44‑1 (MQ=255)
                               atatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAg                                                                <  1:841246/44‑1 (MQ=255)
                                tatGATAATCATTGAAGGCATCCCACAACCCATCATGCACaa                                                                 <  1:2953072/42‑1 (MQ=255)
                                tatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:3416775/49‑1 (MQ=255)
                                tatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:76276/49‑1 (MQ=255)
                                tatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:2695797/49‑1 (MQ=255)
                                tatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:1061106/49‑1 (MQ=255)
                                tatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGc                                    >  1:317569/1‑71 (MQ=255)
                                tatGATAATCATTGAAGGCATCCAACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTACCAAGc                                    >  1:1936586/1‑71 (MQ=255)
                                  tGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                  <  1:3687320/71‑1 (MQ=255)
                                  tGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                  >  1:90736/1‑71 (MQ=255)
                                  tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGa                                                               >  1:632463/1‑42 (MQ=255)
                                  tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGa                                                               >  1:973931/1‑42 (MQ=255)
                                  tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGa                                                               >  1:1370889/1‑42 (MQ=255)
                                  tGATAATCATTGAAGGCAT‑‑CACAACCCATCATGCACAAGa                                                               >  1:1517598/1‑40 (MQ=37)
                                        tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAcc                            <  1:2332220/71‑1 (MQ=255)
                                        tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAcc                            <  1:243413/71‑1 (MQ=255)
                                         cATTGAAGGCATCCCACAACCCATGATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCt                                   >  1:649255/1‑63 (MQ=255)
                                          aTTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaaccaac                                                   >  1:674334/1‑46 (MQ=255)
                                          aTTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaaccaac                                                   >  1:3312011/1‑46 (MQ=255)
                                          aTTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaaccaac                                                   >  1:35714/1‑46 (MQ=255)
                                          aTTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaaccaac                                                   >  1:3512746/1‑46 (MQ=255)
                                          aTTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCgg                          >  1:2242616/1‑71 (MQ=255)
                                          aTTGAAGGCATACCACAACCCATCATGCGCAAGACTGTcaaccaac                                                   >  1:3521370/1‑46 (MQ=255)
                                            tGAAGGCATCCCACAACCCATCATGCGCAAGACTGTcaaccaac                                                   >  1:1565742/1‑44 (MQ=255)
                                            tGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTg                                                 >  1:918119/1‑46 (MQ=255)
                                            tGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTg                                                 >  1:1196214/1‑46 (MQ=255)
                                            tGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTg                                                 >  1:558607/1‑46 (MQ=255)
                                                  cATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTa                  <  1:881861/71‑1 (MQ=255)
                                                  cATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTa                  <  1:3380673/71‑1 (MQ=255)
                                                  cATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTa                  <  1:2858700/71‑1 (MQ=255)
                                                   aTCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAcc                            <  1:3263090/60‑1 (MQ=255)
                                                    tCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGc                                    <  1:1008025/51‑1 (MQ=255)
                                                    tCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGc                                    <  1:3836633/51‑1 (MQ=255)
                                                    tCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGc                                    <  1:403405/51‑1 (MQ=255)
                                                    tCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGc                                    <  1:101407/51‑1 (MQ=255)
                                                    tCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGc                    <  1:1180811/67‑1 (MQ=255)
                                                      ccACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:3886287/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:1965465/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGc                                               >  1:365140/1‑38 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGc                                               >  1:2944602/1‑38 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCaa                                      >  1:909933/1‑47 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCaa                                      >  1:405880/1‑47 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCt                                   >  1:2311364/1‑50 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCTGTGCGGCTAtcag              >  1:2724061/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:3229689/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:2496611/1‑71 (MQ=255)
                                                      ccACAACCCAACATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:2760779/1‑71 (MQ=255)
                                                        acaACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtgtg                                <  1:1055762/51‑1 (MQ=255)
                                                        acaACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtgtg                                <  1:3684989/51‑1 (MQ=255)
                                                          aaCCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagtcag          <  1:2601645/71‑1 (MQ=255)
                                                          aaCCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagtcag          <  1:734802/71‑1 (MQ=255)
                                                            cccATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagtcag          <  1:3142270/69‑1 (MQ=255)
                                                              catcatGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGaa        <  1:185175/69‑1 (MQ=255)
                                                                tcatGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtg    >  1:2152672/1‑71 (MQ=255)
                                                                tcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtg    <  1:1387900/71‑1 (MQ=255)
                                                                  atGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:4084698/1‑71 (MQ=255)
                                                                  atGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:1289057/1‑71 (MQ=255)
                                                                  atGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:1492092/1‑71 (MQ=255)
                                                                  atGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:1649153/70‑1 (MQ=255)
                                                                  atGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:1529927/70‑1 (MQ=255)
                                                                  atGCGCAAGACTGTCAACCAACTGCCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:2171398/70‑1 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtca               >  1:2092094/1‑58 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtca               >  1:2206419/1‑58 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGaa        >  1:3170218/1‑65 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGaa        >  1:3724045/1‑65 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:3943970/1‑71 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:2572015/1‑71 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:3560144/1‑71 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:1075491/1‑71 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:214102/1‑71 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:2079225/70‑1 (MQ=255)
                                                                   tGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:1680714/69‑1 (MQ=255)
                                                                      acaAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:3223414/66‑1 (MQ=255)
                                                                      acaAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:3524383/66‑1 (MQ=255)
                                                                      |                                                                  
TTCGCGAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACATGTG  >  W3110S.gb/2983748‑2983884

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