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	1,043,710	A→G	R146R (CGT→CGC)	gfcC ←	capsule biosynthesis GfcC family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,043,710	0	A	G	100.0%	85.5 / NA	25	R146R (CGT→CGC)	gfcC	capsule biosynthesis GfcC family protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (11/14); total (11/14)

TAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGACGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGATTGAGTAACTGCTGGCGCACGGAT  >  NZ_CP009273/1043574‑1043845

tAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCg                                                                                                                                       <  1:15041/139‑1 (MQ=255)

tAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCg                                                                                                                                       <  2:533936/139‑1 (MQ=255)

 aaTCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGAAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCAGgcgc                                                                                                                                      >  2:110254/1‑139 (MQ=255)

     aCCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTa                                                                                                                                  <  1:110254/139‑1 (MQ=255)

     aCCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTa                                                                                                                                  <  2:184928/139‑1 (MQ=255)

     aCCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTa                                                                                                                                  >  1:60731/1‑139 (MQ=255)

       cATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACg                                                                                                                                >  1:262771/1‑139 (MQ=255)

         tAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGt                                                                                                                              <  1:145609/139‑1 (MQ=255)

                       tCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCCGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGt                                                                                                                >  2:411708/1‑139 (MQ=255)

                                        ggggTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCg                                                                                                                                       >  2:395986/1‑99 (MQ=255)

                                        ggggTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCg                                                                                                                                       <  1:395986/99‑1 (MQ=255)

                                           gTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGCCCCCGACCAACGGGGGATTg                                                                                            <  1:144703/139‑1 (MQ=255)

                                                   gCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTg                                                                                         <  2:108852/134‑1 (MQ=255)

                                                          aTCGGTAACGCTACGGCCCGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACt                                                                             <  1:411708/139‑1 (MQ=255)

                                                                       cGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCa                                                                 <  1:632810/138‑1 (MQ=255)

                                                                             gcctgccAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTc                                                            >  1:281161/1‑137 (MQ=255)

                                                                             gcctgccAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTc                                                            >  1:153546/1‑137 (MQ=255)

                                                                                                cGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGAc                                        >  1:463280/1‑138 (MQ=255)

                                                                                                   ccccAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGt                                    <  1:104183/139‑1 (MQ=255)

                                                                                                             cGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATatt                              >  1:609864/1‑135 (MQ=255)

                                                                                                             agCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGCCCAGTTTGACCGGAAAGCGACCAGTGATatt                              >  2:48518/2‑135 (MQ=255)

                                                                                                                   cagcagAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGATTGAGt                    <  2:281161/139‑1 (MQ=255)

                                                                                                                                gTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGATTGAGTAACTGCTGGCGCa       <  2:609864/139‑1 (MQ=255)

                                                                                                                                   aCCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCg                                          >  1:551424/1‑101 (MQ=255)

                                                                                                                                   aCCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCg                                          <  2:551424/101‑1 (MQ=255)

                                                                                                                                     cGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGATTGAGTAACTGCTGGCGCACGGAt  >  2:177195/1‑139 (MQ=255)

TAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGACGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGATTGAGTAACTGCTGGCGCACGGAT  >  NZ_CP009273/1043574‑1043845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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

CAGGCGTAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGACGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGATTGAGTAACTGCTGGCGCACGGATTTAATCGTTGCCGCC  >  NZ_CP009273/1043568‑1043860

CAGGCGTAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTAC                                                                                                                                                >  SRR3722135.61541/1‑151 (MQ=60)

  GGCGTAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGG                                                                                                                                              >  SRR3722135.266509/1‑151 (MQ=60)

     cgtgggctcggagatgtgtataagagacaGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTAT                                                                                                                                           <  SRR3722135.401486/122‑1 (MQ=60)

     GTAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTAT                                                                                                                                           <  SRR3722135.15243/151‑1 (MQ=60)

          CACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGC                                                                                                                                      <  SRR3722135.111746/151‑1 (MQ=60)

              ATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTAT                                                                                                                                  <  SRR3722135.147649/151‑1 (MQ=60)

                                                GGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGCCCCCGACCAACGGGGGATTGCTGTTCTCATC                                                                                                <  SRR3722135.146731/151‑1 (MQ=60)

                                                               AATCGGTAACGCTACGGCCCGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATC                                                                                 <  SRR3722135.417385/151‑1 (MQ=60)

                                                                        CGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCC                                                                          >  SRR3722135.155670/1‑149 (MQ=60)

                                                                        CGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCC                                                                          >  SRR3722135.285202/1‑149 (MQ=60)

                                                                            ACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTT                                                                     <  SRR3722135.641040/150‑1 (MQ=60)

                                                                                           GGTCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACC                                                      >  SRR3722135.469564/1‑150 (MQ=60)

                                                                                                        GCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGAT                                        <  SRR3722135.105612/151‑1 (MQ=60)

                                                                                                        GCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTG                                            >  SRR3722135.617836/1‑147 (MQ=60)

                                                                                                                              GAGTAATAGTCACCGGGCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATctgtctcttatacacatctccgagccc                   >  SRR3722135.558725/1‑123 (MQ=60)

                                                                                                                                              GCGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGATTGAGTAACTGCTGGCGCACGGATTTAATCGTTGCCGCC  >  SRR3722135.48155/1‑151 (MQ=60)

CAGGCGTAATCACCATAACGTTATTCTTGTCCGCGCCTGCAAGGCGGGGGTGATCTTGCAGATAATCGGTAACGCTACGGCCTGCCTGCCAGGGCAATTGCCCGGCCCCAGAAACCGCACCCAGCAGAGTAATAGTCACCGGACGCTGTACGGTATAGAGCGTATAGTCCCCGACCAACGGGGGATTGCTGTTCTCATCCACTCGTACAAAATCAGGGTCCAGTTTGACCGGTAAGCGACCAGTGATATTGAGATTGAGTAACTGCTGGCGCACGGATTTAATCGTTGCCGCC  >  NZ_CP009273/1043568‑1043860

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`