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
A11 F1 I2 R1 59 52.6 2411032 94.1% 2268781 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 573,440 C→T R24C (CGC→TGC)  rusA → DLP12 prophage, endonuclease RUS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913573,4400CT100.0% 176.2 / NA 51R24C (CGC→TGC) rusADLP12 prophage, endonuclease RUS
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (28/23);  total (28/23)

TGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAGTGCCACATGCCGGATCGCCGTCGCC  >  NC_000913/573309‑573575
                                                                                                                                   |                                                                                                                                       
tGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGtgcacgca                                                                                                                                  >  2:495870/1‑139 (MQ=255)
tGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGtgcacgca                                                                                                                                  >  1:948383/1‑139 (MQ=255)
          aaGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCa                                                                                                                        <  1:1131917/139‑1 (MQ=255)
                     agaACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCaga                                                                                                                      <  2:944283/130‑1 (MQ=255)
                     agaACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCaga                                                                                                                      >  1:944283/1‑130 (MQ=255)
                       aaCACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCAt                                                                                                           >  2:609150/1‑139 (MQ=255)
                               ttATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGAt                                                                                                   <  2:41761/139‑1 (MQ=255)
                                       cTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGc                                                                                           >  1:357989/1‑139 (MQ=255)
                                                  ggTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTa                                                                                >  1:574268/1‑139 (MQ=255)
                                                        taAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACg                                                                          <  1:1020511/139‑1 (MQ=255)
                                                          aGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCa                                                                        <  2:948383/139‑1 (MQ=255)
                                                          aGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCa                                                                        <  1:609150/139‑1 (MQ=255)
                                                            gCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAAt                                                                      >  2:1083830/1‑139 (MQ=255)
                                                            gCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAAt                                                                      >  1:688974/1‑139 (MQ=255)
                                                             cGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGTGGGtgcacg                                                                                                                                    <  1:298332/76‑1 (MQ=255)
                                                             cGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGTGGGtgcacg                                                                                                                                    >  2:298332/1‑76 (MQ=255)
                                                              gTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGc                                                                    >  2:390030/1‑139 (MQ=255)
                                                               tGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCt                                                                   >  2:845709/1‑139 (MQ=255)
                                                                    aCCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGata                                                              <  2:941562/139‑1 (MQ=255)
                                                                     ccTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGatat                                                             <  2:688974/139‑1 (MQ=255)
                                                                     ccTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGatat                                                             <  2:459948/139‑1 (MQ=255)
                                                                      cTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCag                                                                                                                       <  2:192084/80‑1 (MQ=255)
                                                                      cTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCag                                                                                                                       >  1:192084/1‑80 (MQ=255)
                                                                         cAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         >  1:528714/1‑139 (MQ=255)
                                                                         cAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         <  2:357989/139‑1 (MQ=255)
                                                                              tCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATg                                                                     <  2:1076728/122‑1 (MQ=255)
                                                                              tCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATg                                                                     >  1:1076728/1‑122 (MQ=255)
                                                                              tCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGc                                                    <  1:845709/139‑1 (MQ=255)
                                                                              tCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGc                                                    >  2:1014614/1‑139 (MQ=255)
                                                                               cacaTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCt                                                   >  2:163468/1‑139 (MQ=255)
                                                                                      cccTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCtg                                            >  1:193624/1‑139 (MQ=255)
                                                                                      cccTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCtg                                            >  1:249318/1‑139 (MQ=255)
                                                                                      cccTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCC‑GGCTATGCCtgt                                           >  1:725459/1‑139 (MQ=255)
                                                                                          ggCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGaa                                        >  1:228614/1‑139 (MQ=255)
                                                                                           gCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         >  2:195024/1‑121 (MQ=255)
                                                                                           gCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         <  1:195024/121‑1 (MQ=255)
                                                                                           gCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGaaa                                       >  1:1151127/1‑139 (MQ=255)
                                                                                              tCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCaa                                                                       <  2:416517/104‑1 (MQ=255)
                                                                                              tCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCaa                                                                       >  1:416517/1‑104 (MQ=255)
                                                                                                cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAgg                                                                                                                    >  1:345458/1‑57 (MQ=255)
                                                                                                cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAgg                                                                                                                    <  1:1002766/57‑1 (MQ=255)
                                                                                                cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAgg                                                                                                                    >  2:1002766/1‑57 (MQ=255)
                                                                                                cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAgg                                                                                                                    <  2:345458/57‑1 (MQ=255)
                                                                                                cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGggcaggca                                                                                                            >  1:337381/1‑65 (MQ=255)
                                                                                                cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGggcaggca                                                                                                            <  2:337381/65‑1 (MQ=255)
                                                                                                 gAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGc                                 >  1:485674/1‑139 (MQ=255)
                                                                                                       taatCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCt                                                   >  1:510285/1‑115 (MQ=255)
                                                                                                       taatCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCt                                                   <  2:510285/115‑1 (MQ=255)
                                                                                                       taatCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAg                           <  2:574268/139‑1 (MQ=255)
                                                                                                                 tACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCt                                                                   <  1:254812/89‑1 (MQ=255)
                                                                                                                 tACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCt                                                                   >  2:254812/1‑89 (MQ=255)
                                                                                                                        aTAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         >  2:376713/1‑92 (MQ=255)
                                                                                                                        aTAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         <  1:376713/92‑1 (MQ=255)
                                                                                                                                gggTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAGTGCCACATGCCGGAtcgccgtcgcc  >  2:945361/1‑139 (MQ=255)
                                                                                                                                gggTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAGTGCCACATGCCGGAtcgccgtcgcc  <  1:495870/139‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                       
TGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAGTGCCACATGCCGGATCGCCGTCGCC  >  NC_000913/573309‑573575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A