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
A7 F184 I0 R1 46 69.8 1527574 94.8% 1448140 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,440,085 G→T 100% intergenic (‑45/‑891) cspA ← / → xpaC cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,440,0850GT100.0% 153.4 / NA 56intergenic (‑45/‑891)cspA/xpaCcold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (32/24);  total (32/24)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAA  >  CP000730/1439959‑1440218
                                                                                                                              |                                                                                                                                     
cGAATACGTCATTTTTTTTTTTTTTTTTGATAAAGCCGAATCCTTTTTCAGCGTTAAACTATTTAACTGTACCTTGTTTCCTCATCTGAAATCTCCAAGACTAAAATTCATTCATTTTTCTTTTTTTTTTATTACaaaaa                                                                                                                          >  2:237511/1‑140 (MQ=255)
        tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGc                                                                                                                  <  2:736784/140‑1 (MQ=255)
          aTTTTCTCCTTCAAATTAGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAACTTCATTCAATATGCTTATTATCATATTAAAACAAATACATGCaa                                                                                                                >  2:139050/1‑140 (MQ=255)
           ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACATAAAATACATGCaaa                                                                                                               <  2:350902/140‑1 (MQ=255)
                tcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCa                                                                                                          >  1:354516/1‑140 (MQ=255)
                 ccTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc                                                                                                         <  1:741702/140‑1 (MQ=255)
                  cTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACt                                                                                                        <  2:240601/140‑1 (MQ=255)
                       aCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAat                                                                                                   >  1:630757/1‑140 (MQ=255)
                         ttCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAatat                                                                                                 <  1:57378/140‑1 (MQ=255)
                             aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                             >  2:38866/1‑140 (MQ=255)
                             aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                             >  2:205895/1‑140 (MQ=255)
                               aaaGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg                                                                                           >  1:124047/1‑140 (MQ=255)
                                  gCCGAATCCTTTTTCAGCGTTAAACAATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAAACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAATTAAATCAAATATTCTTTGCaa                                                                                        >  2:703292/1‑140 (MQ=255)
                                         ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATATCACTCAAATATTATTTGCAATATGGaa                                                                                 >  1:260849/1‑140 (MQ=255)
                                          cTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACATCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGAAAATTTCACTCAAATATTCTTTGCAATATGGaat                                                                                >  1:143417/1‑140 (MQ=255)
                                              ttttttttttttccATTTAACTGTACCTTGTTTCATAATCTGAATTCTCCAAGACTAAAATTCATTCACTATGCTTATTCTCATCTTTCTATTATTTCTTGCAAATTTCACTCAAATATTCTTTCCAATATGGAGTAatc                                                                            >  2:435839/13‑140 (MQ=255)
                                              tttttttttAAACCATTTAACAGTACCTTGTTTCATAATCTGAAACCTCCAAGACTGAAATTAATTCAATATTCTTATTCTCATATTTCAAAAAATATATGCAAATTTCAATCCAATATTTTTTGCAATATGGAATAatc                                                                            >  2:258099/8‑140 (MQ=255)
                                                cAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                          <  2:232964/140‑1 (MQ=255)
                                                cAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                          <  1:454588/140‑1 (MQ=255)
                                                cAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                          <  1:43172/140‑1 (MQ=255)
                                                  gtgtaaatctaTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCt                                                                        <  2:683433/130‑1 (MQ=255)
                                                    gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCGAATTTCACTCAAATATTCTTTACAATATAGAATAATAATTTGc                                                                      >  1:152990/1‑140 (MQ=255)
                                                    gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGc                                                                      >  1:70782/1‑140 (MQ=255)
                                                    gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACCCAAATATTCTTTGCAATATGGAATAATCATCTGc                                                                      >  2:15067/1‑140 (MQ=255)
                                                     ttAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt                                                                     <  2:354516/140‑1 (MQ=255)
                                                      tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt                                                                    <  1:523449/140‑1 (MQ=255)
                                                      tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAACACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt                                                                    <  2:195395/140‑1 (MQ=255)
                                                      tAAAACATTTAAGCGTAACTTGTGCTTGAATCTGAAACCTCCAAGATTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt                                                                    <  1:203536/140‑1 (MQ=255)
                                                           cATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACtt                                                               >  2:743708/1‑140 (MQ=255)
                                                            aTTTAACTGCACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGTAATAATCATCTGCTTactaca                                                              <  2:196453/140‑6 (MQ=255)
                                                              ttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGta                                                            <  2:679489/140‑1 (MQ=255)
                                                               tAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACCCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat                                                           <  1:15067/140‑1 (MQ=255)
                                                                 aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTACATTGtatta                                                         >  2:519516/1‑140 (MQ=255)
                                                                      aCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTg                                                    >  1:218810/1‑140 (MQ=255)
                                                                      aCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTg                                                    <  1:480761/140‑1 (MQ=255)
                                                                      aCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTg                                                    >  1:571719/1‑140 (MQ=255)
                                                                         tagtataaTAATCTGCAACCTCCAAGACTAAAATTCATTCAATATTCTTATGCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg                                                 >  2:444159/8‑140 (MQ=255)
                                                                           gTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                               <  1:38866/140‑1 (MQ=255)
                                                                           gTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                               <  1:205895/140‑1 (MQ=255)
                                                                                 tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTAcc                                         >  1:383856/1‑140 (MQ=255)
                                                                                 tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTAcc                                         >  2:471861/1‑140 (MQ=255)
                                                                                        aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc                                  >  2:71584/1‑140 (MQ=255)
                                                                                        aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATAAGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc                                  >  1:200105/1‑140 (MQ=255)
                                                                                         aaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATATATGCAAATTTCACTCGAAGATTCTTTGACATATGGAATTATCATATGCTTATATTGTATTATTGTGAAGTTATTTTCAAAtatta                                 >  1:109506/1‑136 (MQ=255)
                                                                                         aaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGGAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATGATAGTGCAGTTATTACCAAATTGca                                 >  1:465052/1‑140 (MQ=255)
                                                                                            cTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaata                              >  1:694970/1‑140 (MQ=255)
                                                                                                  gACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAGAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACaataa                        <  1:127565/140‑1 (MQ=255)
                                                                                                              ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTc            >  1:498680/1‑140 (MQ=255)
                                                                                                               tcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCCCTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa           <  2:124047/140‑1 (MQ=255)
                                                                                                                caATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCAt          >  2:553995/1‑140 (MQ=255)
                                                                                                                    atacTTATTCTCATATTACAAAAAATAAATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa      >  2:727806/4‑140 (MQ=255)
                                                                                                                    atGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTCAACTGTATTATTGTGTTGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa      <  2:310683/140‑1 (MQ=255)
                                                                                                                    atGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa      >  2:93686/1‑140 (MQ=255)
                                                                                                                    atGCTTATTCTCATATTAAAAAAAACTTATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACAAAATTGCAATACAATCATAAACAATATTCATTTaa      >  2:349432/1‑140 (MQ=255)
                                                                                                                        ttattaTCAAATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATATATCAGTTATTACCAAATTGCAATACAATAATAAGAAATATTCATTTAATCaa  <  2:194397/140‑1 (MQ=255)
                                                                                                                        ttATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCaa  <  2:12235/140‑1 (MQ=255)
                                                                                                                              |                                                                                                                                     
CGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAA  >  CP000730/1439959‑1440218

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A