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 741,621 G→A 31.3% L40L (TTG→TTA)  ycfL → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE741,6210GA31.3% 82.5 / 41.5 89L40L (TTG→TTA) ycfLhypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (31/30);  new base A (17/11);  total (48/41)
Fisher's exact test for biased strand distribution p-value = 4.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

GTTCACATCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGCATC  >  minE/741560‑741683
                                                             |                                                              
gTTCACATCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCg                                                          >  1:33526/1‑68 (MQ=255)
       tCCGGTAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:3184549/69‑1 (MQ=255)
       tCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:1092789/69‑1 (MQ=255)
       tCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:2759405/69‑1 (MQ=255)
       tCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:1234058/69‑1 (MQ=255)
       tCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:2624694/69‑1 (MQ=255)
       tCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:1293732/69‑1 (MQ=255)
       tCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:2430818/69‑1 (MQ=255)
       tCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:2236517/69‑1 (MQ=255)
       tCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  <  1:2085555/69‑1 (MQ=255)
         cGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  >  1:943472/1‑67 (MQ=255)
         cGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAg                                                  >  1:1453001/1‑67 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:2891414/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:2164083/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:2285776/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:1376652/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:2078273/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:1338694/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:2523941/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:1875867/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:2677370/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:1787338/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:2941893/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:3193587/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:342092/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:1640553/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:3429980/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:65222/1‑68 (MQ=255)
           gAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTAGCTGCGGGCATCAGTGc                                               >  1:823994/1‑68 (MQ=255)
                tCCGGTGAATGATGAGCAATCGCTGGTGATGGATTCATCTTTATTGGc                                                              >  1:259085/1‑48 (MQ=255)
                tCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGc                                                              >  1:3351757/1‑48 (MQ=255)
                tCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGc                                                              >  1:2634685/1‑48 (MQ=255)
                tCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGc                                                              >  1:853390/1‑48 (MQ=255)
                 ccGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAg                                        >  1:2795946/1‑69 (MQ=255)
                     tGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCcct                                    <  1:2739/69‑1 (MQ=255)
                       aaTGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCccttc                                  <  1:1418724/69‑1 (MQ=255)
                       aaTGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCccttc                                  <  1:942427/69‑1 (MQ=255)
                                     gCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGa                    <  1:884371/69‑1 (MQ=255)
                                     gCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGa                    <  1:2653893/69‑1 (MQ=255)
                                     gCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGa                    <  1:1826271/69‑1 (MQ=255)
                                     gCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGa                    <  1:1731746/69‑1 (MQ=255)
                                     gCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGa                    <  1:1657322/69‑1 (MQ=255)
                                           gATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTc               <  1:1083389/68‑1 (MQ=255)
                                           gATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTc               <  1:1222732/68‑1 (MQ=255)
                                           gATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTc               <  1:1649702/68‑1 (MQ=255)
                                           gATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTc               <  1:121887/68‑1 (MQ=255)
                                            aTGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTc               <  1:1835018/67‑1 (MQ=255)
                                            aTGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCaa             >  1:2234606/1‑69 (MQ=255)
                                            aTGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCaa             >  1:1512012/1‑69 (MQ=255)
                                               gAGTGATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCa              >  1:3262052/1‑65 (MQ=255)
                                               gAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGcc                                      >  1:3252463/1‑41 (MQ=255)
                                               gAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCa              >  1:3206626/1‑65 (MQ=255)
                                               gAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCa              >  1:1635187/1‑65 (MQ=255)
                                               gAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCa              >  1:1618192/1‑65 (MQ=255)
                                               gAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCa              >  1:3108822/1‑65 (MQ=255)
                                               gAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCa              >  1:1931287/1‑65 (MQ=255)
                                               gAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCa              >  1:2398956/1‑65 (MQ=255)
                                               gAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCa              >  1:1345071/1‑65 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:2162632/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:2249304/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:2851442/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:2879174/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:868530/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:2138903/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:2578952/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:2192322/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:3418972/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:545161/69‑1 (MQ=255)
                                                 gTCATCTTTATTAGCTGCGGGCATCAGTGCAGAAAAGCCCGTCCTTTCGACATCTGATATTCAACCTTc        <  1:567686/69‑1 (MQ=255)
                                                   cATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAg      <  1:485179/69‑1 (MQ=255)
                                                   cATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAg      <  1:2117900/69‑1 (MQ=255)
                                                   cATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAg      <  1:2008891/69‑1 (MQ=255)
                                                   cATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAg      <  1:3200768/69‑1 (MQ=255)
                                                   cATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAg      <  1:1723090/69‑1 (MQ=255)
                                                   cATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAg      <  1:1792119/69‑1 (MQ=255)
                                                   cATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAg      <  1:1443804/69‑1 (MQ=255)
                                                    aTCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGc     >  1:1112079/1‑69 (MQ=255)
                                                    aTCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGc     >  1:2066923/1‑69 (MQ=255)
                                                      cTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGc     <  1:3432634/67‑1 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:67954/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:3188580/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:2927325/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:125463/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTACCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:430558/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTACCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:245387/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTACCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:1483792/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTACCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:2128462/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTACCTTTCGACGTCTGATATTCAACCTTCAGCATc  >  1:1858719/1‑69 (MQ=255)
                                                       tttATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTACCTTTCGACGTCTGATATTCAACCTTCAGAATc  >  1:1837583/1‑69 (MQ=255)
                                                             |                                                              
GTTCACATCCGGAAATTCCGGTGAATGATGAGCAATCGCTGGTGATGGAGTCATCTTTATTGGCTGCGGGCATCAGTGCAGAAAAGCCCTTCCTTTCGACGTCTGATATTCAACCTTCAGCATC  >  minE/741560‑741683

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