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
A8 F1 I2 R1 765 53.2 2691310 93.4% 2513683 103.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,190,144 G→A P102S (CCG→TCG)  phoP ← response regulator in two‑component regulatory system with PhoQ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,190,1440GA100.0% 180.7 / NA 57P102S (CCG→TCG) phoPresponse regulator in two‑component regulatory system with PhoQ
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/27);  total (30/27)

TTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCT  >  NC_000913/1190010‑1190278
                                                                                                                                      |                                                                                                                                      
ttCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTa                                                                                                                                    >  1:174091/1‑139 (MQ=255)
 tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAg                                                                                                                                   >  2:952018/1‑139 (MQ=255)
  cGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑GGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTc                                                                                                                                 <  2:346326/139‑1 (MQ=255)
              aTAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTcaca                                                                                                                              <  2:125483/131‑1 (MQ=255)
              aTAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTcaca                                                                                                                              >  1:125483/1‑131 (MQ=255)
                  ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCa                                                                                                                  >  1:269710/1‑139 (MQ=255)
                  ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCa                                                                                                                  >  1:541948/1‑139 (MQ=255)
                  ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCa                                                                                                                  >  1:953922/1‑139 (MQ=255)
                   tCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCAc                                                                                                                 <  1:952018/139‑1 (MQ=255)
                   tCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCAGCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCAc                                                                                                                 <  2:953922/139‑1 (MQ=255)
                             agagaTCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTaa                                                                                                       >  1:741765/1‑139 (MQ=255)
                                  tCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACtt                                                                                                  <  2:741765/139‑1 (MQ=255)
                                                 gggAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGc                                                                                    >  2:372760/1‑138 (MQ=255)
                                                 gggAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGc                                                                                    <  1:372760/138‑1 (MQ=255)
                                                             aCCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:672053/139‑1 (MQ=255)
                                                             aCCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:1142968/139‑1 (MQ=255)
                                                              ccTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       >  1:123250/1‑138 (MQ=255)
                                                              ccTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:123250/138‑1 (MQ=255)
                                                                tgtgAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       >  1:1042085/1‑136 (MQ=255)
                                                                tgtgAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:1042085/136‑1 (MQ=255)
                                                                          gACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAg                                                          >  1:59692/1‑139 (MQ=255)
                                                                                  ttACGCCCCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCa                                                  <  2:269710/139‑1 (MQ=255)
                                                                                     cgccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:802198/115‑1 (MQ=255)
                                                                                     cgccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGAATTTGTCCTGCCAGCTTTCACggg                                                                       >  1:802198/1‑115 (MQ=255)
                                                                                       ccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAat                                                                                                                          <  1:490624/62‑1 (MQ=255)
                                                                                       ccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAat                                                                                                                          >  2:490624/1‑62 (MQ=255)
                                                                                          cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAAt                                                       <  2:981111/126‑1 (MQ=255)
                                                                                          cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAAt                                                       >  1:981111/1‑126 (MQ=255)
                                                                                          cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACa                                          >  2:524197/1‑139 (MQ=255)
                                                                                              aaTGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGt                                      <  1:524197/139‑1 (MQ=255)
                                                                                               aTGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGtt                                     >  1:328877/1‑139 (MQ=255)
                                                                                                    tGCATTCGCGCCATCACCTCTTCAATATGAACCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCgg                                                    <  1:354251/119‑1 (MQ=255)
                                                                                                    tGCATTCGCGCCATCACCTCTTCAATATGAACCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCgg                                                    >  2:354251/1‑119 (MQ=255)
                                                                                                    tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTc                                                                                                                                 <  1:345987/42‑1 (MQ=255)
                                                                                                    tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTc                                                                                                                                 >  2:345987/1‑42 (MQ=255)
                                                                                                    tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCAc                                                                                                                 <  2:1253117/58‑1 (MQ=255)
                                                                                                    tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCAc                                                                                                                 >  1:1253117/1‑58 (MQ=255)
                                                                                                    tGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTAc                                >  2:863344/1‑139 (MQ=255)
                                                                                                     gCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:1107767/99‑1 (MQ=255)
                                                                                                     gCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       >  1:1107767/1‑99 (MQ=255)
                                                                                                      cATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGc                              >  2:176121/1‑139 (MQ=255)
                                                                                                            cgcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACtt                                                                                                         <  2:289299/58‑1 (MQ=255)
                                                                                                            cgcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACtt                                                                                                         >  1:289299/1‑58 (MQ=255)
                                                                                                             gcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAgcggc                       <  2:541948/139‑1 (MQ=255)
                                                                                                                aTCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               <  2:1116753/48‑1 (MQ=255)
                                                                                                                aTCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               >  1:1116753/1‑48 (MQ=255)
                                                                                                                aTCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGaa                    >  1:1001217/1‑139 (MQ=255)
                                                                                                                 tCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAAt                   <  2:174091/139‑1 (MQ=255)
                                                                                                                              atGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCg      <  2:328877/139‑1 (MQ=255)
                                                                                                                               tGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGt     <  1:176121/139‑1 (MQ=255)
                                                                                                                               tGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGt     >  1:953430/1‑139 (MQ=255)
                                                                                                                                gAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTc    >  1:1185869/1‑139 (MQ=255)
                                                                                                                                  aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTcc                                                                                       >  2:468773/1‑54 (MQ=255)
                                                                                                                                  aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTcc                                                                                       <  1:468773/54‑1 (MQ=255)
                                                                                                                                  aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTGCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCt  >  2:134987/1‑139 (MQ=255)
                                                                                                                                  aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGt                                                                   <  1:364340/74‑1 (MQ=255)
                                                                                                                                  aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGt                                                                   >  2:364340/1‑74 (MQ=255)
                                                                                                                                      |                                                                                                                                      
TTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCT  >  NC_000913/1190010‑1190278

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