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
A2 F5 I179 R1	182	40.3	1547118	96.8%	1497610	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	625,777	A→G	D143G (GAC→GGC)	cstA →	pyruvate/proton symporter CstA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	625,777	0	A	G	100.0%	124.0 / NA	35	D143G (GAC→GGC)	cstA	pyruvate/proton symporter CstA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/22); total (13/22)

AGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCT  >  NZ_CP009273/625643‑625906

aGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGt                                                                                                                               <  2:288998/139‑1 (MQ=255)

aGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGt                                                                                                                               <  2:229978/139‑1 (MQ=255)

     gTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGtcgctc                                                                                                                          <  1:14339/139‑1 (MQ=255)

     gTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGtcgctc                                                                                                                          <  1:268353/139‑1 (MQ=255)

     gTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGtcgctc                                                                                                                          >  1:464615/1‑139 (MQ=255)

      tCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGtcgctcg                                                                                                                         <  1:418203/139‑1 (MQ=255)

                    cGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGt                                                                                                           <  2:606279/139‑1 (MQ=255)

                            gcggcgCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAaag                                                                                                      >  2:485315/1‑136 (MQ=255)

                                                 ccGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCgggg                                                                              >  1:639962/1‑139 (MQ=255)

                                                       atgatCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTg                                                                        >  2:759132/1‑139 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:99182/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  2:420442/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  2:32564/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:375659/137‑1 (MQ=255)

                                                                          gggTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTa                                                      <  2:464615/138‑1 (MQ=255)

                                                                               gtTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCa                                                <  2:744073/139‑1 (MQ=255)

                                                                                  ctcGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATgg                                             >  1:679729/1‑139 (MQ=255)

                                                                                         gtgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTAt                                      >  1:664080/1‑139 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCt                                                            >  1:49267/1‑116 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCt                                                            <  2:49267/116‑1 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTa                                                      >  1:109621/1‑122 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTa                                                      <  2:109621/122‑1 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATc                                     >  1:237951/1‑139 (MQ=255)

                                                                                              gtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTg                                 <  2:639962/139‑1 (MQ=255)

                                                                                                   ggATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTg                            <  1:485315/139‑1 (MQ=255)

                                                                                                   ggATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTg                            <  2:471666/139‑1 (MQ=255)

                                                                                                         cATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:719025/99‑1 (MQ=255)

                                                                                                         cATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              >  2:719025/1‑99 (MQ=255)

                                                                                                         cATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGc                       >  1:680266/1‑138 (MQ=255)

                                                                                                                             cgcgCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGcc    <  2:679729/137‑1 (MQ=255)

                                                                                                                             cgcgCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCt  <  2:26610/139‑1 (MQ=255)

                                                                                                                                gcCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGa         <  2:374635/129‑1 (MQ=255)

                                                                                                                                gcCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGa         >  1:374635/1‑129 (MQ=255)

                                                                                                                                 ccGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGa                                                   >  2:510697/1‑86 (MQ=255)

                                                                                                                                 ccGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGa                                                   <  1:510697/86‑1 (MQ=255)

AGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCT  >  NZ_CP009273/625643‑625906

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TGCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACT  >  NZ_CP009273/625637‑625910

TGCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCG                                                                                                                             >  SRR3722133.470916/1‑151 (MQ=60)

          GGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGC                                                                                                                   <  SRR3722133.14502/151‑1 (MQ=60)

          GGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGC                                                                                                                   <  SRR3722133.272004/151‑1 (MQ=60)

           GTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCT                                                                                                                  <  SRR3722133.423973/151‑1 (MQ=60)

                                            TGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGG                                                                                 >  SRR3722133.648334/1‑151 (MQ=60)

                                                                      cgtgggctcggagatgtgtataagagacaGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                       <  SRR3722133.728351/122‑1 (MQ=60)

                                                                        GCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                       <  SRR3722133.380911/149‑1 (MQ=60)

                                                                        GCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                       <  SRR3722133.100474/149‑1 (MQ=60)

                                                                             CTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGT                                                >  SRR3722133.688547/1‑151 (MQ=60)

                                                                                    agtacggtctcgtgggctcggagatgtgtataagagacagGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATT                                            <  SRR3722133.517576/108‑1 (MQ=60)

                                                                                    GGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATC                                         >  SRR3722133.672738/1‑151 (MQ=60)

                                                                                     GTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCctgtctcttatac                                        >  SRR3722133.49883/1‑138 (MQ=60)

                                                                                     GTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCctgtctc                                        >  SRR3722133.111099/1‑144 (MQ=60)

                                                                                     GTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCC                                        >  SRR3722133.241177/1‑151 (MQ=60)

                                                                                                    GTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCG                          >  SRR3722133.689091/1‑150 (MQ=60)

                                                                                                        AGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGAT                     <  SRR3722133.491867/151‑1 (MQ=60)

                                                                                                                           TGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACT  >  SRR3722133.379873/1‑151 (MQ=60)

TGCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACT  >  NZ_CP009273/625637‑625910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`