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 I181 R1	159	32.7	1279082	96.9%	1239430	121.0

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%	116.3 / NA	33	D143G (GAC→GGC)	cstA	pyruvate/proton symporter CstA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/21); total (12/21)

AGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCT  >  NZ_CP009273/625643‑625906

aGCAGGTCCGCTGGTGGGTCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTCCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGt                                                                                                                               <  2:336476/139‑1 (MQ=255)

  cAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGtcg                                                                                                                             <  1:539698/139‑1 (MQ=255)

     gTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGtcgctc                                                                                                                          >  2:615115/1‑139 (MQ=255)

     gTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGgcgctc                                                                                                                          >  2:567203/1‑139 (MQ=255)

      tCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGtcgctcg                                                                                                                         >  2:490091/1‑139 (MQ=255)

                gggCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAg                                                                                                                <  1:405258/138‑1 (MQ=255)

                     ggTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTc                                                                                                          <  1:126007/139‑1 (MQ=255)

                            gcggcgCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAaag                                                                                                      >  2:125001/1‑136 (MQ=255)

                                      tGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGcc                                                                                         <  2:30718/139‑1 (MQ=255)

                                                               gctgctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCtg                                                                   <  2:276477/136‑1 (MQ=255)

                                                                ctgctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCtggtgg                                                               >  1:415063/1‑139 (MQ=255)

                                                                   ctCGCTGGGGTTGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:346837/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:490091/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  2:393427/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:561753/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:509797/137‑1 (MQ=255)

                                                                          gggTGGTTCTCGCCGGTGCGGTGCAGGATTTGATGTTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCATCCGGCGGGGTGATTGCGCTGGTGGCCTGCTTTa                                                      <  2:271404/138‑1 (MQ=255)

                                                                          gggTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTa                                                      <  1:541232/138‑1 (MQ=255)

                                                                                ttCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCAt                                               <  1:495321/139‑1 (MQ=255)

                                                                                     gCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGt                                            <  1:330203/137‑1 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATc                                     >  2:506339/1‑139 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATc                                     >  2:413645/1‑139 (MQ=255)

                                                                                              gtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTg                                 <  1:174170/139‑1 (MQ=255)

                                                                                              gtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTg                                 <  2:396045/139‑1 (MQ=255)

                                                                                                         cATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAg                                                                                                                >  1:126196/1‑49 (MQ=255)

                                                                                                         cATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAg                                                                                                                <  2:126196/49‑1 (MQ=255)

                                                                                                         cATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGc                       >  1:78767/1‑138 (MQ=255)

                                                                                                                cTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGAt                                                  <  1:578876/104‑1 (MQ=255)

                                                                                                                cTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGAt                                                  >  2:578876/1‑104 (MQ=255)

                                                                                                                        ttCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGcc                                                                                         <  2:366401/57‑1 (MQ=255)

                                                                                                                        ttCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGcc                                                                                         >  1:366401/1‑57 (MQ=255)

                                                                                                                             cgcgCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCt  >  2:214264/1‑139 (MQ=255)

                                                                                                                             cgcgCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCt  <  1:506339/139‑1 (MQ=255)

AGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCT  >  NZ_CP009273/625643‑625906

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACTCATAGCCCGTGGGG  >  NZ_CP009273/625644‑625924

GCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTG                                                                                                                                    <  SRR3722135.546841/151‑1 (MQ=60)

              GGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGA                                                                                                                       <  SRR3722135.410850/150‑1 (MQ=60)

                   CGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGAT                                                                                                                 <  SRR3722135.127777/151‑1 (MQ=60)

                                                    GGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGC                                                                                >  SRR3722135.420773/1‑151 (MQ=60)

                                                                 GCTCGCTGGGGTTGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                                     <  SRR3722135.351745/149‑1 (MQ=60)

                                                                 GCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                                     <  SRR3722135.496663/149‑1 (MQ=60)

                                                                 GCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                                     <  SRR3722135.569167/149‑1 (MQ=60)

                                                                 GCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                                     <  SRR3722135.516613/149‑1 (MQ=60)

                                                                        GGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTC                                                             <  SRR3722135.548395/150‑1 (MQ=60)

                                                                           gctcggagatgtgtataagagacaGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTA                                                         <  SRR3722135.586498/127‑1 (MQ=60)

                                                                              GTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCC                                                      <  SRR3722135.501941/151‑1 (MQ=60)

                                                                                   CGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTG                                                   <  SRR3722135.334909/149‑1 (MQ=60)

                                                                                            GGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCG                                        <  SRR3722135.176587/151‑1 (MQ=60)

                                                                                             GTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGActgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaaaaaaa                                        >  SRR3722135.127968/1‑71 (MQ=60)

                                                                                             GTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCG                                        >  SRR3722135.79838/1‑150 (MQ=60)

                                                                                                            GTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaa                         >  SRR3722135.371561/1‑79 (MQ=60)

                                                                                                                           ACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACTCATAGCC         <  SRR3722135.513123/151‑1 (MQ=60)

                                                                                                                             GCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACTCATAGCCCG       >  SRR3722135.645487/1‑151 (MQ=60)

                                                                                                                                  GTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACTCATAGCCCGTGGGG  <  SRR3722135.126755/151‑1 (MQ=60)

GCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACTCATAGCCCGTGGGG  >  NZ_CP009273/625644‑625924

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`