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
A14 F1 I1 R1 770 68.5 3470224 91.7% 3182195 103.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,598,557 A→G *368Q (TAA→CAA)  livJ ← branched‑chain amino acid ABC transporter periplasmic binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,598,5570AG100.0% 193.4 / NA 54*368Q (TAA→CAA) livJbranched‑chain amino acid ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/26);  total (28/26)

TGTGTTGCAATTTACTGATTTCTTTGGATCTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTACTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCGGTCCCATTACGGTATCCACGGAGTTCGCTTTCAGGT  >  NC_000913/3598430‑3598682
                                                                                                                               |                                                                                                                             
tgtgtTGCAATTTACTGATTTCTTTGGATCTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCgg                                                                                                                    >  1:1214399/1‑139 (MQ=255)
         aTTTACTGATTTCTTTGGATCTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCgccgtgc                                                                                                           <  2:1214399/139‑1 (MQ=255)
                 aTTTCTTTGGATCTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCg                                                                                                   >  1:182132/1‑139 (MQ=255)
                                        gATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCtt                                                                                                                            <  2:1555880/91‑1 (MQ=255)
                                        gATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCtt                                                                                                                            >  1:1555880/1‑91 (MQ=255)
                                        gATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCg                                                                                                   >  2:1697283/1‑116 (MQ=255)
                                        gATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCg                                                                                                   <  1:1697283/116‑1 (MQ=255)
                                        gATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTc                                                                            >  1:895129/1‑139 (MQ=255)
                                        gATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTc                                                                            >  1:605093/1‑139 (MQ=255)
                                        gATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTc                                                                            >  1:842130/1‑139 (MQ=255)
                                               cGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCt                                                                     <  1:246015/139‑1 (MQ=255)
                                                gTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCtt                                                                    >  2:335838/1‑139 (MQ=255)
                                                  ttACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGc                                                                                                >  2:400207/1‑109 (MQ=255)
                                                  ttACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGc                                                                                                <  1:400207/109‑1 (MQ=255)
                                                   tACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCgccg                                                                                                              >  2:492099/1‑94 (MQ=255)
                                                   tACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCgccg                                                                                                              <  1:492099/94‑1 (MQ=255)
                                                     cgccgcATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGa                                                               <  2:842130/139‑1 (MQ=255)
                                                     cgccgcATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGa                                                               <  2:895129/139‑1 (MQ=255)
                                                         gcATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTTGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGTATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGc                                                           <  2:562432/139‑1 (MQ=255)
                                                          cATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTg                                                                                                 <  2:1043231/100‑1 (MQ=255)
                                                          cATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTg                                                                                                 >  1:1043231/1‑100 (MQ=255)
                                                           aTCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCt                                                         >  1:743080/1‑139 (MQ=255)
                                                               ggCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTtct                                                     <  2:182132/139‑1 (MQ=255)
                                                                              aCTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCg                                      <  1:335838/139‑1 (MQ=255)
                                                                               cTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCgg                                     >  2:929340/1‑139 (MQ=255)
                                                                                   atatTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCGGTccc                                 >  1:1593331/1‑139 (MQ=255)
                                                                                       tAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCtt                                                                                                                            <  2:994955/44‑1 (MQ=255)
                                                                                       tAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCtt                                                                                                                            >  1:994955/1‑44 (MQ=255)
                                                                                       tAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCGGTCCCATTa                             <  2:1593331/139‑1 (MQ=255)
                                                                                          cAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCg                                                                                                                     <  1:1374075/48‑1 (MQ=255)
                                                                                          cAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCg                                                                                                                     >  2:1374075/1‑48 (MQ=255)
                                                                                          cAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGt                                           <  1:24105/122‑1 (MQ=255)
                                                                                          cAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGt                                           >  2:24105/1‑122 (MQ=255)
                                                                                            aTTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCa                                                                           >  2:623034/1‑88 (MQ=255)
                                                                                            aTTTGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCa                                                                           <  1:623034/88‑1 (MQ=255)
                                                                                             tttGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTtct                                                     <  2:154092/109‑1 (MQ=255)
                                                                                             tttGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTtct                                                     >  1:154092/1‑109 (MQ=255)
                                                                                              ttGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAg                                                                <  2:1150156/97‑1 (MQ=255)
                                                                                              ttGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAg                                                                >  1:1150156/1‑97 (MQ=255)
                                                                                              ttGGCGGCAACCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCGGTCCCATTACGGTATc                      >  2:1076466/1‑139 (MQ=255)
                                                                                                       aCCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGt                                                                                            >  2:123069/1‑60 (MQ=255)
                                                                                                       aCCCAAAGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGt                                                                                            <  1:123069/60‑1 (MQ=255)
                                                                                                           aaaGTTGCCGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCGGTCCCATTACGGTATCCACGGAGTTCGCt         <  2:743080/139‑1 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGcc                                                                                  >  1:852665/1‑59 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGcc                                                                                  <  2:852665/59‑1 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCa                                                                           <  2:1023897/66‑1 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCa                                                                           >  1:1023897/1‑66 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCGGATCGCCTTTCTCATCCGAGGTCAGCGGTCCCATTACGGTATcc                     >  2:1114386/1‑120 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGcc                                                          >  2:1080313/1‑83 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGcc                                                          <  1:1080313/83‑1 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCGGTCCCATTACGGTATcc                     <  1:1114386/120‑1 (MQ=255)
                                                                                                                  ccGATTAATGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCGGTCCCATTACGGTATCCACGGAGTTCGCTTTCAGGt  >  1:107115/1‑139 (MQ=255)
                                                                                                                        aaTGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAg                                                                        >  2:284357/1‑63 (MQ=255)
                                                                                                                        aaTGATTGCTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAg                                                                        <  1:284357/63‑1 (MQ=255)
                                                                                                                               |                                                                                                                             
TGTGTTGCAATTTACTGATTTCTTTGGATCTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGAAGCAACGTACTCGATATTAGCAATTTGGCGGCAACCCAAAGTTGCCGATTAATGATTACTTCGCATCGGTCGCCGTGCCGTTGGCGTGCCAGTCAAATACGCCGAACTCAAAGCCTTTCAGATCGCCTTTCTCATCCCAGGTCAGCGGTCCCATTACGGTATCCACGGAGTTCGCTTTCAGGT  >  NC_000913/3598430‑3598682

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A