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 F174 I1 R1 26 63.3 1412239 95.2% 1344451 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
JC USA300TCH1516_ALE 2,709,677 Δ12 bp coding (1239‑1250/1812 nt) oatA_2 ← O‑acetyltransferase OatA

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 270967612 (0.190)51 (0.810) 45/280 0.6 81.6% coding (1251/1812 nt) oatA_2 O‑acetyltransferase OatA
?USA300TCH1516_ALE 2709689 = 11 (0.180)coding (1238/1812 nt) oatA_2 O‑acetyltransferase OatA

AGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2709538‑2709676
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTTTAGGTAAAAATGCAAA  >  USA300TCH1516_ALE/2709689‑2709825
                                                                                                                                                                                                                                                                                    
AGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATT                                                                                                                                         <  2:109988/141‑1
    AAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCT                                                                                                                                     <  1:324973/141‑1
     AGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTT                                                                                                                                    <  1:671341/141‑1
               AATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGC                                                                                                                          >  1:385615/1‑141
                 TATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTT                                                                                                                        <  1:732395/141‑1
                  tTCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTC                                                                                                                       <  1:41663/140‑1
                  ATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTC                                                                                                                       <  1:535656/141‑1
                   TCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCA                                                                                                                      <  2:407318/141‑1
                    CCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCAT                                                                                                                     <  1:610273/141‑1
                             CCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGC                                                                                                            >  1:977969/1‑141
                              CGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCC                                                                                                           <  2:187185/141‑1
                               GAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCA                                                                                                          >  2:80060/1‑141
                                 GTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAG                                                                                                        <  1:859847/141‑1
                                   CACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTG                                                                                                      <  1:128851/141‑1
                                      CAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCAT                                                                                                   <  2:305315/141‑1
                                      CAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCAT                                                                                                   >  1:675762/1‑141
                                       AATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGCCTGCCTCTCCTCTTGCTCATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCCCTTTTTTCTCGGCTTCATGTTGTTTGCCACGTGCATC                                                                                                  >  1:325709/1‑141
                                             TAGTGGTGATGACTTTTTACTATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTG                                                                                            <  1:211195/141‑1
                                             TAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTG                                                                                            <  1:487552/141‑1
                                             TAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTG                                                                                            <  1:211210/141‑1
                                              AGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGT                                                                                           >  1:203649/1‑141
                                                              TAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGA                                                                           >  1:929275/1‑141
                                                               AATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGAT                                                                          >  1:74478/1‑141
                                                                  ATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATCGA                                                                       >  1:525709/1‑141
                                                                  ATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGA                                                                       <  1:347419/141‑1
                                                                   TCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGAC                                                                      >  1:402935/1‑141
                                                                    CCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACG                                                                     >  1:893419/1‑141
                                                                       CTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAA                                                                  <  1:677920/141‑1
                                                                       CTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAA                                                                  <  1:302103/141‑1
                                                                               TTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCCAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAAT                                                          >  2:206888/1‑141
                                                                               TTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAAT                                                          >  1:176165/1‑141
                                                                                TCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATA                                                         <  1:196098/141‑1
                                                                                      TCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAA                                                   >  1:369867/1‑141
                                                                                           TTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGACTCCAGTATAGGATAACTAAC                                              >  1:52907/1‑141
                                                                                           TTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAAC                                              <  1:756187/141‑1
                                                                                                 TCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTT                                        >  2:174505/1‑141
                                                                                                  CTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTC                                       <  1:140956/141‑1
                                                                                                     GCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAG                                    <  2:315813/141‑1
                                                                                                      CTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGC                                   <  1:74090/141‑1
                                                                                                          TCTTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAAT                               >  1:122957/1‑141
                                                                                                            TTTTTTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTG                             >  1:37327/1‑141
                                                                                                                TTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCC                         <  2:278175/141‑1
                                                                                                                TTAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCC                         >  2:405891/1‑141
                                                                                                                 TAACGACTTTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCT                        <  1:894488/141‑1
                                                                                                                         TTTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTTTA                >  1:700272/1‑141
                                                                                                                          TTTTCTTCGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTTTAG               >  1:219424/1‑141
                                                                                                                                 CGTTGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTTTAGGTAAAAA        >  1:533203/1‑141
                                                                                                                                    TGTTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTTTAGGTAAAAATGC     >  1:813510/1‑141
                                                                                                                                      TTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCACACTGTCCCCTGAGCCCACCGCTAGCCGCAACCCATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTTTAGGTAAAAATGCAA   <  1:93146/141‑1
                                                                                                                                      TTTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTTTAGGTAAAAATGCAA   <  1:90140/141‑1
                                                                                                                                       TTTATTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTCTAGGTAAAAATGCAAA  <  1:623074/141‑1
                                                                                                                                                                                                                                                                                    
AGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2709538‑2709676
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCATCAAACTGTCCACTGAGCACAACGATAGACGGAACCAATAATAGGATAACTAACACTGTTCTAGCAAATTGCCCCTTCTTTTTAGGTAAAAATGCAAA  >  USA300TCH1516_ALE/2709689‑2709825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A