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 1,133,571 G→A 28.4% T68T (ACC→ACT)  ydiY ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,133,5710GA28.4% 74.4 / 27.2 70T68T (ACC→ACT) ydiYconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (26/24);  new base A (14/6);  total (40/30)
Fisher's exact test for biased strand distribution p-value = 1.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTAGAAGAAGTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATT  >  minE/1133505‑1133639
                                                                  |                                                                    
atTAGAAGAAGTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCAtggt                                                                    <  1:3054427/69‑1 (MQ=255)
atTAGAAGAAGTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCAtggt                                                                    <  1:2945093/69‑1 (MQ=255)
atTAGAAGAAGTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCAtggt                                                                    <  1:1561322/69‑1 (MQ=255)
   agaagaAGTATTACTGGCGTTCCCCCCCAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATggtggt                                                                 >  1:2398193/1‑69 (MQ=255)
   agaagaAGTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATggtggt                                                                 >  1:3200908/1‑69 (MQ=255)
   agaagaAGTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATggtggt                                                                 >  1:809236/1‑69 (MQ=255)
   agaagaAGTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATggtggt                                                                 >  1:2356169/1‑69 (MQ=255)
      agaagTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTc                                                              <  1:2647525/69‑1 (MQ=255)
             ttACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGt                                                        >  1:2446205/1‑68 (MQ=255)
             ttACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTa                                                       >  1:327389/1‑69 (MQ=255)
             ttACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTa                                                       >  1:2427589/1‑69 (MQ=255)
             ttACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTa                                                       >  1:1545869/1‑69 (MQ=255)
             ttACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTa                                                       >  1:1637058/1‑69 (MQ=255)
             ttACTGGCGTTCCCCCACAGCGACCAGGCACTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTa                                                       >  1:556394/1‑69 (MQ=255)
               aCTGGCTTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTaa                                                      >  1:7021/1‑68 (MQ=255)
               aCTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATTCCAGGTCATGGTGGTGTCAGCCGTaa                                                      >  1:3327089/1‑68 (MQ=255)
               aCTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTaa                                                      >  1:716699/1‑68 (MQ=255)
                        cccccACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCt                                            >  1:2422002/1‑69 (MQ=255)
                        cccccACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCt                                            >  1:1587285/1‑69 (MQ=255)
                        cccccAAAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCt                                            >  1:317/1‑69 (MQ=255)
                             acaGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCg                                       <  1:2300890/69‑1 (MQ=255)
                              caGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:2012776/69‑1 (MQ=255)
                              caGAGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:1401243/69‑1 (MQ=255)
                                             ggtgTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATtgt                         >  1:3381737/1‑67 (MQ=255)
                                             ggtgTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATtgt                         >  1:2712278/1‑67 (MQ=255)
                                             ggtgTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATtgt                         >  1:1181509/1‑67 (MQ=255)
                                             ggtgTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATtg                          >  1:1418304/1‑66 (MQ=255)
                                             ggtgAGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATtgt                         >  1:1187925/1‑67 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:2441639/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:2806524/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:2845301/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:2439582/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:1809863/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:2139490/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:2002121/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:1776746/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:1592143/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:1580432/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:600649/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:619955/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:818135/53‑1 (MQ=255)
                                              gtgtgtCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      <  1:1091143/53‑1 (MQ=255)
                                                 tgtCCATACCATGTCATAGTGGTGTCAGCCGTAAGt                                                    >  1:213388/1‑36 (MQ=38)
                                                 tgtCCATACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGc                       >  1:266760/1‑65 (MQ=255)
                                                 tgtCCATACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGa                   >  1:3040596/1‑69 (MQ=255)
                                                 tgtCCATACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGa                   >  1:1072463/1‑69 (MQ=255)
                                                 tgtCCATACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGa                   >  1:523711/1‑69 (MQ=255)
                                                 tgtCCATACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGa                   >  1:848355/1‑69 (MQ=255)
                                                 tgtCCATACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGa                   >  1:2367611/1‑69 (MQ=255)
                                                 tgtCCATACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGa                   >  1:2292659/1‑69 (MQ=255)
                                                 tgtCCATACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGa                   >  1:1352763/1‑69 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCATCCGTAATTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAg                    <  1:2543105/66‑1 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      >  1:2414672/1‑48 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      >  1:3329336/1‑48 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      >  1:14647/1‑48 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCaat                    <  1:1906509/66‑2 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAg                    <  1:1670638/66‑1 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAg                    <  1:387858/66‑1 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGata                 >  1:3313266/1‑69 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGata                 >  1:1733082/1‑69 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGata                 >  1:1462234/1‑69 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGata                 >  1:835329/1‑69 (MQ=255)
                                                   tCCATACCAGGTCATGGTGGTGTCAGCCCTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAg                    <  1:2966706/66‑1 (MQ=255)
                                                       tACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCt             >  1:1011618/1‑69 (MQ=255)
                                                       tACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCt             >  1:2524803/1‑69 (MQ=255)
                                                       tACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCt             >  1:2969853/1‑69 (MQ=255)
                                                       tACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCt             >  1:2236888/1‑69 (MQ=255)
                                                       tACCAGGTCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCt             >  1:2899569/1‑69 (MQ=255)
                                                         ccAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGt                                      >  1:2474721/1‑42 (MQ=255)
                                                              tCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCa      <  1:184438/69‑1 (MQ=255)
                                                              tCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCa      <  1:3397147/69‑1 (MQ=255)
                                                              tCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCa      <  1:2166663/69‑1 (MQ=255)
                                                              tCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCa      <  1:162187/69‑1 (MQ=255)
                                                              tCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCa      <  1:1432302/69‑1 (MQ=255)
                                                              tCATAGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCa      <  1:114692/69‑1 (MQ=255)
                                                               cATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCa      >  1:2077155/1‑68 (MQ=255)
                                                               cATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCa      <  1:605532/68‑1 (MQ=255)
                                                                  ggtggtGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGAtt  <  1:904072/69‑1 (MQ=255)
                                                                  ggtggtGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGAtt  <  1:851494/69‑1 (MQ=255)
                                                                  ggtggtGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGAtt  <  1:2771765/69‑1 (MQ=255)
                                                                  ggtggtGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGAtt  <  1:1118046/69‑1 (MQ=255)
                                                                  ggtggtGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGAtt  <  1:1547709/69‑1 (MQ=255)
                                                                  ggtggtGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGAtt  <  1:468923/69‑1 (MQ=255)
                                                                  ggtggtGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGAtt  <  1:2143497/69‑1 (MQ=255)
                                                                  ggtggtGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCATGATTGTGCAAGATATCCTGCGTTCAGAtt  <  1:3200724/69‑1 (MQ=255)
                                                                  |                                                                    
ATTAGAAGAAGTATTACTGGCGTTCCCCCACAGCGACCAGGCAGTGGTGTGTCCATACCAGGTCATGGTGGTGTCAGCCGTAAGTGAGGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATT  >  minE/1133505‑1133639

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