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
A12 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,594,132 (C)8→9 pseudogene (3856/3861 nt) yneO ← pseudogene, AidA homolog

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,594,1241.C100.0% 164.7 / NA 47pseudogene (2/1461 nt)yneOpseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (24/23);  total (24/23)

TTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCC  >  NC_000913/1594001‑1594255
                                                                                                                            |                                                                                                                                    
ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCAt                                                                                                                       >  1:1103685/1‑139 (MQ=255)
ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCA‑TCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATa                                                                                                                      >  1:1173648/1‑139 (MQ=255)
      ccGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGtt                                                                                                                 >  1:721461/1‑139 (MQ=255)
         gTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCAATTCTCCAGGTTGCCGCCGTTAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                              <  2:721461/139‑1 (MQ=255)
                 gCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTg                                                                                                      <  2:35020/139‑1 (MQ=255)
                   cGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCa                                                                                                    >  1:707604/1‑139 (MQ=255)
                    gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                              >  2:952300/1‑128 (MQ=255)
                    gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                              <  1:952300/128‑1 (MQ=255)
                    gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAg                                                                                                   >  1:365864/1‑139 (MQ=255)
                            tCAGTACA‑TCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACAt                                                                                          >  1:427370/1‑139 (MQ=255)
                              aGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTg                                                                                                                                       >  2:360034/1‑94 (MQ=255)
                              aGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTg                                                                                                                                       <  1:360034/94‑1 (MQ=255)
                               gTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACAttt                                                                                        >  2:1076158/1‑139 (MQ=255)
                                    ttCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGa                                                                                   <  2:203346/139‑1 (MQ=255)
                                     tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                              >  2:914369/1‑111 (MQ=255)
                                     tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                              <  1:914369/111‑1 (MQ=255)
                                     tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGAc                                                                                  >  1:1480200/1‑139 (MQ=255)
                                     tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCACGTTGCCGCCGATAGTGGATTTCGCGACACGCAGTGCCCCCCCCCCAGGCCTAACGTTGATTTCACCTGCCGCGGTGAGTTTTCCCGa                                                                                   >  2:730762/1‑139 (MQ=255)
                                         cGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATca                                                                              <  1:989588/139‑1 (MQ=255)
                                          ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATcac                                                                             >  1:629546/1‑139 (MQ=255)
                                           gTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGTCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATcaca                                                                            <  2:1229830/139‑1 (MQ=255)
                                           gTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCA‑TCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                           <  2:1173648/139‑1 (MQ=255)
                                            ttttCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                           <  2:707604/139‑1 (MQ=255)
                                              tCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                         <  2:427370/139‑1 (MQ=255)
                                               ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCg                                                                                    <  2:1155518/127‑1 (MQ=255)
                                               ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCg                                                                                    >  1:1155518/1‑127 (MQ=255)
                                                 ccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                      <  1:1204991/123‑1 (MQ=255)
                                                 ccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                      >  2:1204991/1‑123 (MQ=255)
                                                    cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGATTTAGCGACACGCAGTGCCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt                                                                    <  1:730762/139‑1 (MQ=255)
                                                      tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                         <  1:228419/131‑1 (MQ=255)
                                                      tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                         >  2:228419/1‑131 (MQ=255)
                                                               aTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATa                                                                                                                      <  2:1196618/77‑1 (MQ=255)
                                                               aTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATa                                                                                                                      >  1:1196618/1‑77 (MQ=255)
                                                                 ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCAt                                                                                                                       >  2:738250/1‑74 (MQ=255)
                                                                 ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCAt                                                                                                                       <  1:738250/74‑1 (MQ=255)
                                                                 ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATa                                                                                                                      <  2:797597/75‑1 (MQ=255)
                                                                 ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATa                                                                                                                      >  1:797597/1‑75 (MQ=255)
                                                                      ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGa                                                 >  1:113677/1‑139 (MQ=255)
                                                                       cGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGAc                                                <  2:1480200/139‑1 (MQ=255)
                                                                        gTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACt                                               <  2:365864/139‑1 (MQ=255)
                                                                           ccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGc                                            >  2:736112/1‑139 (MQ=255)
                                                                                         gTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCag                              <  2:1103685/139‑1 (MQ=255)
                                                                                            gccgccGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCACTGTTAt                                                                  >  2:644697/1‑100 (MQ=255)
                                                                                            gccgccGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTGCATATCACCTGCAGTGGTGACATTTCCCGTCATCACACCACTGTTAt                                                                  <  1:644697/100‑1 (MQ=255)
                                                                                              cgccgATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACa                                                                                           <  2:253192/74‑1 (MQ=255)
                                                                                              cgccgATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACa                                                                                           >  1:253192/1‑74 (MQ=255)
                                                                                              cgccgATAGTGGTTTTAGCGACACGCAGTG‑‑ccccccc                                                                                                                              <  1:764711/37‑1 (MQ=255)
                                                                                              cgccgATAGTGGTTTTAGCGACACGCAGTG‑‑ccccccc                                                                                                                              >  2:764711/1‑37 (MQ=255)
                                                                                                                  acacGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTcccc     >  1:155705/1‑139 (MQ=255)
                                                                                                                   cacGCAGTGC‑CCCCCCCCAGGCCTAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTTACTTGCCTTATTAATGGCAGCGTCGGAACCGAAACCAATTTccccc    >  1:1129729/1‑139 (MQ=255)
                                                                                                                     cGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTccccccc  <  2:113677/139‑1 (MQ=255)
                                                                                                                            |                                                                                                                                    
TTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCC  >  NC_000913/1594001‑1594255

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A