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	525,225	A→G	pseudogene (248/366 nt)	ylbG ←	helix‑turn‑helix domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	525,225	0	A	G	100.0%	130.6 / NA	36	pseudogene (248/366 nt)	ylbG	helix‑turn‑helix domain‑containing protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (20/16); total (20/16)

GTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACG  >  NZ_CP009273/525099‑525360

gTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCg                                                                                                                              <  2:583119/138‑1 (MQ=255)

gTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCg                                                                                                                              <  1:561461/138‑1 (MQ=255)

 ttCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTa                                                                                                                            <  1:698757/139‑1 (MQ=255)

      tATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATcaa                                                                                                                       >  2:596507/1‑139 (MQ=255)

           tCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATcaacaa                                                                                                                    >  2:344865/1‑137 (MQ=255)

                tGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTg                                                                                                             >  2:512788/1‑139 (MQ=255)

                                   gAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTa                                                                                          <  2:69950/139‑1 (MQ=255)

                                    aGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTAc                                                                                         <  1:512788/139‑1 (MQ=255)

                                      tAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTAc                                                                                         >  2:637739/1‑137 (MQ=255)

                                      tAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTAc                                                                                         <  1:637739/137‑1 (MQ=255)

                                       aaCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGt                                                                                      >  2:657471/1‑139 (MQ=255)

                                        aCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTAc                                                                                         <  2:416034/135‑1 (MQ=255)

                                        aCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTAc                                                                                         >  1:416034/1‑135 (MQ=255)

                                        aCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGtt                                                                                     >  1:519480/1‑139 (MQ=255)

                                            gacagaACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTa                                                                                 <  2:473089/139‑1 (MQ=255)

                                                 aaCGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCACGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTAAGTTGCCTCATCGGTACGGTTCTTAAGGt                                                                             >  2:638395/1‑138 (MQ=255)

                                                       caccacTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAgc                                                                      >  1:135170/1‑139 (MQ=255)

                                                           acTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCgcgg                                                                  <  2:326536/139‑1 (MQ=255)

                                                                  gagaTAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTAc                                                           >  1:473297/1‑139 (MQ=255)

                                                                  gagaTAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTAc                                                           >  2:331483/1‑139 (MQ=255)

                                                                         aaaCCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGc                                                                                                                <  2:327385/79‑1 (MQ=255)

                                                                         aaaCCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGc                                                                                                                >  1:327385/1‑79 (MQ=255)

                                                                         aaaCCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAAt                                                    <  2:503963/139‑1 (MQ=255)

                                                                                       cGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCcaca                                       <  2:135170/138‑1 (MQ=255)

                                                                                        gCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACg                                                                                        <  1:243804/88‑1 (MQ=255)

                                                                                        gCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACg                                                                                        >  2:243804/1‑88 (MQ=255)

                                                                                           gCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCAt                                                                                               <  1:769047/78‑1 (MQ=255)

                                                                                           gCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCAt                                                                                               >  2:769047/1‑78 (MQ=255)

                                                                                           gCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGcc                                  >  1:370283/1‑139 (MQ=255)

                                                                                                   cTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGa                          <  1:331483/139‑1 (MQ=255)

                                                                                                      gCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTAc                                                                                         <  2:707086/73‑1 (MQ=255)

                                                                                                      gCCCGGCGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTAc                                                                                         >  1:707086/1‑73 (MQ=255)

                                                                                                                gACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGt              >  2:77964/1‑138 (MQ=255)

                                                                                                                 aCCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTaa            >  1:42053/1‑139 (MQ=255)

                                                                                                                      gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAt        >  1:365327/1‑138 (MQ=255)

                                                                                                                      gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAt        >  1:318616/1‑138 (MQ=255)

                                                                                                                           ggggAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACg  >  2:725712/1‑139 (MQ=255)

GTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACG  >  NZ_CP009273/525099‑525360

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `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

TGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCG  >  NZ_CP009273/525098‑525369

TGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAAC                                                                                                                            <  SRR3722133.568926/150‑1 (MQ=60)

 GTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAG                                                                                                                          <  SRR3722133.707804/151‑1 (MQ=60)

                              atacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTC                                                                                             <  SRR3722133.778981/100‑1 (MQ=60)

                              GTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTC                                                                                             >  SRR3722133.526482/1‑151 (MQ=60)

                              GTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTC                                                                                             >  SRR3722133.421781/1‑151 (MQ=60)

                                    GAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGG                                                                                       <  SRR3722133.646090/151‑1 (MQ=60)

                                    GAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGG                                                                                       <  SRR3722133.519679/151‑1 (MQ=60)

                                      agtacggtctcgtgggctcggagatgtgtataagagacagCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGT                                                                                      <  SRR3722133.247101/110‑1 (MQ=60)

                                             GACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCG                                                                              >  SRR3722133.136931/1‑151 (MQ=60)

                                                        CACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACG                                                                   >  SRR3722133.479716/1‑151 (MQ=60)

                                                               GTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCtgtctcttatacacatctccgagcccacgagaccgtactagatctcgt                                                             >  SRR3722133.331935/1‑102 (MQ=60)

                                                                                 CTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCT                                          >  SRR3722133.375462/1‑151 (MQ=60)

                                                                                            GCTCGTTGCTGGCCCGGCGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgt                               >  SRR3722133.716208/1‑95 (MQ=60)

                                                                                                   GCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGG                        <  SRR3722133.336152/151‑1 (MQ=60)

                                                                                                       GCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAAC                    >  SRR3722133.42577/1‑151 (MQ=60)

                                                                                                            GTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATA                >  SRR3722133.370452/1‑150 (MQ=60)

                                                                                                            GTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATA                >  SRR3722133.323014/1‑150 (MQ=60)

                                                                                                                          TCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCG  >  SRR3722133.294534/1‑150 (MQ=60)

TGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCG  >  NZ_CP009273/525098‑525369

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: `‑`