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 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,806,042 (C)6→7 coding (42/759 nt) ydiY ← acid‑inducible putative outer membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,806,0361.C100.0% 140.4 / NA 40G16G (GGC→GGG) ydiYacid‑inducible putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (18/22);  total (18/22)

GAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGAA  >  NC_000913/1805902‑1806166
                                                                                                                                       |                                                                                                                                  
gagCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccc                                                                                                                                <  1:739263/139‑1 (MQ=255)
     tttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgc                                                                                                                           <  2:1520494/139‑4 (MQ=255)
               ccTGATTGTGCAAGATACCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACg                                                                                                                  <  2:820677/139‑1 (MQ=255)
                   aTTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgc                                                                                                                           <  2:1271317/125‑4 (MQ=255)
                   aTTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgc                                                                                                                           >  1:1271317/1‑122 (MQ=255)
                         cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGaa                                                                                                        >  1:1158785/1‑139 (MQ=255)
                         cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGaa                                                                                                        >  2:1004239/1‑139 (MQ=255)
                         cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGaa                                                                                                        <  1:450885/139‑1 (MQ=255)
                                 ccTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTc                                                                                                >  1:1241813/1‑139 (MQ=255)
                                         cAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCtt                                                                                        <  2:283849/139‑1 (MQ=255)
                                         cAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCtt                                                                                        <  2:1430030/139‑1 (MQ=255)
                                          aGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTc                                                                                       >  1:824047/1‑139 (MQ=255)
                                            aTTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAAc                                                                                                                        >  2:190211/1‑104 (MQ=255)
                                            aTTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAAc                                                                                                                        <  1:190211/104‑1 (MQ=255)
                                                          gTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCg                                                                       <  2:142248/139‑1 (MQ=255)
                                                                  gcgcTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTAcaacaa                                                               <  2:824047/139‑1 (MQ=255)
                                                                     cTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa                                                                               >  1:1527502/1‑120 (MQ=255)
                                                                     cTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa                                                                               <  2:1527502/120‑1 (MQ=255)
                                                                         cAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAaga                                                        <  2:1241813/139‑1 (MQ=255)
                                                                                       aCAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTcc                                          >  1:870493/1‑139 (MQ=255)
                                                                                        cAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCtt                                                                                        >  1:800262/1‑92 (MQ=255)
                                                                                        cAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCtt                                                                                        <  2:800262/92‑1 (MQ=255)
                                                                                           tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAAc                                                                                                                        >  1:1262613/1‑57 (MQ=255)
                                                                                           tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAAc                                                                                                                        <  2:1262613/57‑1 (MQ=255)
                                                                                           tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGc                                                                                          <  1:1503478/87‑1 (MQ=255)
                                                                                           tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGc                                                                                          >  2:1503478/1‑87 (MQ=255)
                                                                                           tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgcc                                                                                                                          <  2:1195986/54‑5 (MQ=255)
                                                                                           tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgcc                                                                                                                          >  1:1195986/1‑50 (MQ=255)
                                                                                                   gAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGGCCCGGAAACTTTCt                              >  2:734257/1‑139 (MQ=255)
                                                                                                    aaTCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCtt                             >  1:1409644/1‑139 (MQ=255)
                                                                                                     atcatcGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTa                            >  2:1528328/1‑139 (MQ=255)
                                                                                                         tcGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAg                                                                                           >  1:1536904/1‑72 (MQ=255)
                                                                                                         tcGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAg                                                                                           <  2:1536904/72‑1 (MQ=255)
                                                                                                              aGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCaaa                   >  1:241362/1‑139 (MQ=255)
                                                                                                                cTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTac                                                                    >  1:295873/1‑88 (MQ=255)
                                                                                                                cTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTac                                                                    <  2:295873/88‑1 (MQ=255)
                                                                                                                cTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTa                            >  2:1460819/1‑128 (MQ=255)
                                                                                                                cTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTa                            <  1:1460819/128‑1 (MQ=255)
                                                                                                                   cATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATGTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTa              <  2:241362/139‑1 (MQ=255)
                                                                                                                    aTTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAg             <  2:1409644/139‑1 (MQ=255)
                                                                                                                    aTTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAg             <  1:1528328/139‑1 (MQ=255)
                                                                                                                     ttCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGCCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGc            <  2:870493/139‑1 (MQ=255)
                                                                                                                       cAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGt          <  2:1158785/139‑1 (MQ=255)
                                                                                                                          tGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATcgcg                                              >  1:1301343/1‑100 (MQ=255)
                                                                                                                          tGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATcgcg                                              <  2:1301343/100‑1 (MQ=255)
                                                                                                                               cAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGaa  <  1:1004239/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                  
GAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGAA  >  NC_000913/1805902‑1806166

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A