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
A9 F1 I1 R1 64 69.7 3300380 93.4% 3082554 111.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,863,165 T→C R277R (CGT→CGC)  ygbK → FliA‑regulated DUF1537 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,863,1650TC94.3% 174.5 / 0.3 53R277R (CGT→CGC) ygbKFliA‑regulated DUF1537 family protein
Reads supporting (aligned to +/- strand):  ref base T (3/0);  new base C (23/27);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 1.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.22e-01

GGGCGCAAGAAAACGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGTGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCAGCACTGACGCATTGGC  >  NC_000913/2863032‑2863299
                                                                                                                                     |                                                                                                                                      
gggCGCAAGAAAACGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGt                                                                                                                                   >  2:922883/1‑139 (MQ=255)
 ggCGCAAGAAAACGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGtt                                                                                                                                  >  1:1499935/1‑139 (MQ=255)
          aaaCGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCa                                                                                                                         <  1:1107078/139‑1 (MQ=255)
           aaCGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCAc                                                                                                                        >  2:1502424/1‑139 (MQ=255)
                tAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGc                                                                                                                   >  1:828594/1‑139 (MQ=255)
                tAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGc                                                                                                                   >  2:1053624/1‑139 (MQ=255)
                tAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGc                                                                                                                   >  1:35078/1‑139 (MQ=255)
                  aCCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCct                                                                                                                 <  2:1042520/139‑1 (MQ=255)
                   ccAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCctc                                                                                                                <  1:1272635/139‑1 (MQ=255)
                   ccAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCctc                                                                                                                <  1:181575/139‑1 (MQ=255)
                     aGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCtctc                                                                                                              <  1:78020/139‑1 (MQ=255)
                     aGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCtctc                                                                                                              <  2:133109/139‑1 (MQ=255)
                     aGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCtctc                                                                                                              <  1:1127269/139‑1 (MQ=255)
                            cAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGaa                                                                                                       >  2:839333/1‑139 (MQ=255)
                            cAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGaa                                                                                                       >  2:882252/1‑139 (MQ=255)
                               aGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGGCCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAAct                                                                                                    <  2:1404374/139‑1 (MQ=255)
                                   gggCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGTGAAGCTGATGTGGCACGCTGCCTCTCAATTGAAACTCTgg                                                                                                >  2:927121/1‑139 (MQ=255)
                                   gggCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTgg                                                                                                <  1:1598664/139‑1 (MQ=255)
                                    ggCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCtctc                                                                                                              <  2:646280/124‑1 (MQ=255)
                                    ggCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCtctc                                                                                                              >  1:646280/1‑124 (MQ=255)
                                         ccGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAAct                                                                                                    >  2:1055105/1‑129 (MQ=255)
                                         ccGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAAct                                                                                                    <  1:1055105/129‑1 (MQ=255)
                                         ccGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCtt                                                                                          >  2:1414993/1‑139 (MQ=255)
                                            ctcgctGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATg                                                                                       <  1:359297/139‑1 (MQ=255)
                                                  gggCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATAACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACg                                                                                 <  1:1414993/139‑1 (MQ=255)
                                                      gcggcgTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGTGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACt                                                                             >  1:719153/1‑139 (MQ=255)
                                                         gcgTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGc                                                                          >  2:1446145/1‑139 (MQ=255)
                                                                   ctcCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGtt                                                                <  1:882252/139‑1 (MQ=255)
                                                                    tcCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCa                                                                                                                         >  2:41833/1‑81 (MQ=255)
                                                                    tcCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCa                                                                                                                         <  1:41833/81‑1 (MQ=255)
                                                                        gTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTggg                                                           <  1:1053624/139‑1 (MQ=255)
                                                                           cATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCa                                                        <  2:828594/139‑1 (MQ=255)
                                                                              gCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGt                                                                                                                                   <  1:1620280/61‑1 (MQ=255)
                                                                              gCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGt                                                                                                                                   >  2:1620280/1‑61 (MQ=255)
                                                                                   cAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAgtg                                                >  2:340304/1‑139 (MQ=255)
                                                                                            aaCCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGca                                                                                     <  1:67680/93‑1 (MQ=255)
                                                                                            aaCCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGca                                                                                     >  1:668334/1‑93 (MQ=255)
                                                                                            aaCCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGca                                                                                     >  2:67680/1‑93 (MQ=255)
                                                                                            aaCCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGca                                                                                     <  2:668334/93‑1 (MQ=255)
                                                                                            aaCCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTg                                          <  2:1238001/136‑1 (MQ=255)
                                                                                            aaCCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTg                                          >  1:1238001/1‑136 (MQ=255)
                                                                                              ccGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGc                                                                                                                      >  1:1878/1‑58 (MQ=255)
                                                                                              ccGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGc                                                                                                                      <  2:1878/58‑1 (MQ=255)
                                                                                              ccGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCa                                     >  2:1036711/1‑139 (MQ=255)
                                                                                                                ccGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGc                                                                                            >  1:141103/1‑66 (MQ=255)
                                                                                                                ccGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGc                                                                                            <  2:141103/66‑1 (MQ=255)
                                                                                                                 cGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCa                  <  2:35078/139‑1 (MQ=255)
                                                                                                                   tCAAATTGCACCAGCCCGTGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCAGc                >  1:907494/1‑139 (MQ=255)
                                                                                                                   tCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGca                                                                                     <  2:661751/70‑1 (MQ=255)
                                                                                                                   tCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGca                                                                                     >  1:661751/1‑70 (MQ=255)
                                                                                                                           cACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCAC‑CGAACTGGCAGAGCGGGTTCTGGGCCAGGAAAGTGTACTTTCTCCACTGGTTTTTGCCACCGCCAGCACTGACGCa       >  1:1235478/1‑139 (MQ=255)
                                                                                                                              cAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCAGCACTGACGCAtt     <  1:469160/139‑1 (MQ=255)
                                                                                                                                 cccGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCAAGCACTGACGCATTGgc  <  2:778079/139‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                      
GGGCGCAAGAAAACGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGTGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCAGCACTGACGCATTGGC  >  NC_000913/2863032‑2863299

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A