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	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%	116.2 / NA	32	pseudogene (248/366 nt)	ylbG	helix‑turn‑helix domain‑containing protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/17); total (15/17)

AAATTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAA  >  NZ_CP009273/525093‑525350

aaaTTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCg                                                                                                                          <  2:280037/138‑1 (MQ=255)

       ttCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTa                                                                                                                  <  1:369317/139‑1 (MQ=255)

              tCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATcaaca                                                                                                           <  2:409757/139‑1 (MQ=255)

                 tCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATcaacaa                                                                                                          >  1:605737/1‑137 (MQ=255)

                      tGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTg                                                                                                   >  2:200290/1‑139 (MQ=255)

                          aTTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCa                                                                                               <  2:421626/139‑1 (MQ=255)

                                aaGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGTTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGc                                                                                          <  2:618413/138‑1 (MQ=255)

                                          aGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTAc                                                                               <  1:192793/139‑1 (MQ=255)

                                              aCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGtt                                                                           >  1:421617/1‑139 (MQ=255)

                                              aCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGtt                                                                           >  2:82599/1‑139 (MQ=255)

                                              aCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGtt                                                                           >  2:241522/1‑139 (MQ=255)

                                              aCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGtt                                                                           >  1:277036/1‑139 (MQ=255)

                                                 agacagaACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCtt                                                                        <  1:195146/139‑1 (MQ=255)

                                                 agacagaACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCtt                                                                        <  1:241522/139‑1 (MQ=255)

                                                 agacagaACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTCCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCtt                                                                        <  2:421617/139‑1 (MQ=255)

                                                      gaACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGt                                                                   <  2:290211/139‑1 (MQ=255)

                                                       aaCGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGt                                                                   >  1:367104/1‑138 (MQ=255)

                                                                          gaTAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGa                                               >  2:87875/1‑139 (MQ=255)

                                                                                  cccccTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTg                                       <  1:82599/139‑1 (MQ=255)

                                                                                     ccTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTgcgc                                    <  1:180224/139‑1 (MQ=255)

                                                                                       tGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCAt                                  >  1:400882/1‑139 (MQ=255)

                                                                                                 gCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGcc                        >  2:321798/1‑139 (MQ=255)

                                                                                                   tCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTg                                       <  2:517272/122‑1 (MQ=255)

                                                                                                   tCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTg                                       >  1:517272/1‑122 (MQ=255)

                                                                                                            gCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTg                                       <  2:347996/113‑1 (MQ=255)

                                                                                                            gCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTg                                       >  1:347996/1‑113 (MQ=255)

                                                                                                            gCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGAc               <  2:400882/137‑1 (MQ=255)

                                                                                                                 gTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGAc                                                    <  2:463671/95‑1 (MQ=255)

                                                                                                                 gTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGAc                                                    >  1:463671/1‑95 (MQ=255)

                                                                                                                       aCCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTaa  >  1:537139/1‑139 (MQ=255)

                                                                                                                            gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAAt                                          <  2:306881/94‑1 (MQ=255)

                                                                                                                            gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAAt                                          >  1:306881/1‑94 (MQ=255)

AAATTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAA  >  NZ_CP009273/525093‑525350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `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

GAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAA  >  NZ_CP009273/525078‑525356

GAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGA                                                                                                                                    >  SRR3722135.294375/1‑149 (MQ=60)

                     GTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAG                                                                                                             <  SRR3722135.374506/151‑1 (MQ=60)

                     GTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAAC                                                                                                               >  SRR3722135.613662/1‑149 (MQ=60)

                                                  GTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTC                                                                                >  SRR3722135.427399/1‑151 (MQ=60)

                                                  GTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTC                                                                                >  SRR3722135.281027/1‑151 (MQ=60)

                                                        GAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGG                                                                          <  SRR3722135.195526/151‑1 (MQ=60)

                                                           TAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTT                                                                        >  SRR3722135.372271/1‑150 (MQ=60)

                                                               CAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAG                                                                   <  SRR3722135.244939/151‑1 (MQ=60)

                                                               CAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAG                                                                   <  SRR3722135.197904/151‑1 (MQ=60)

                                                                                           TAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATC                                       >  SRR3722135.406435/1‑151 (MQ=60)

                                                                                                ACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACAC                                  <  SRR3722135.83710/151‑1 (MQ=60)

                                                                                                   CCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGC                               <  SRR3722135.182726/151‑1 (MQ=60)

                                                                                                       GTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCtgtctc                           >  SRR3722135.524142/1‑145 (MQ=60)

                                                                                                                GCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCtgtctcttatacac                   >  SRR3722135.352925/1‑136 (MQ=60)

                                                                                                                     TTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCctgtctcttatacacatctccgagcccacgagac             >  SRR3722135.469961/1‑117 (MQ=60)

                                                                                                                          GGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaaaaggccataaagaccttcccattgtcgct        >  SRR3722135.482378/1‑48 (MQ=60)

                                                                                                                           GCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAAC       >  SRR3722135.544243/1‑151 (MQ=60)

                                                                                                                                GTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACtgtctcttatacacatctccgagcccacgagacc  >  SRR3722135.311278/1‑117 (MQ=60)

GAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATAA  >  NZ_CP009273/525078‑525356

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`