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
A1 F4 I96 R1	227	23.3	882352	98.0%	864704	126.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	635,449	T→C	S81P (TCC→CCC)	ahpF →	alkyl hydroperoxide reductase subunit F

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	635,449	0	T	C	100.0%	108.4 / NA	31	S81P (TCC→CCC)	ahpF	alkyl hydroperoxide reductase subunit F
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/17); total (14/17)

AAGGAACTGTTGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCTCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGATTTTGAATTCGAAACCTATTAC  >  NZ_CP009273/635317‑635583

aaGGAACTGTTGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGc                                                                                                                                  <  1:29109/139‑1 (MQ=255)

         ttGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCa                                                                                                                           <  1:347348/137‑1 (MQ=255)

         ttGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCAc                                                                                                                          >  2:321976/1‑138 (MQ=255)

                aaaTCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCAc                                                                                                                  <  2:128112/139‑1 (MQ=255)

                     gCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCg                                                                                                              <  1:321976/138‑1 (MQ=255)

                     gCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGc                                                                                                             <  1:12683/139‑1 (MQ=255)

                     gCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGc                                                                                                             <  2:298763/139‑1 (MQ=255)

                              tCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTgg                                                                                                    >  2:88724/1‑139 (MQ=255)

                              tCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTgg                                                                                                    >  1:240935/1‑139 (MQ=255)

                                aGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCg                                                                                                  <  2:188796/139‑1 (MQ=255)

                                        tCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTg                                                                                               >  1:330263/1‑134 (MQ=255)

                                        tCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTg                                                                                               <  2:330263/134‑1 (MQ=255)

                                           ccTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGAc                                                                                       <  1:331063/139‑1 (MQ=255)

                                           ccTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGAc                                                                                       <  2:96281/139‑1 (MQ=255)

                                                              cTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGa                                                                      >  1:6336/1‑137 (MQ=255)

                                                                tGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAaag                                                                   >  2:337994/1‑138 (MQ=255)

                                                                        cGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGt                                                          >  2:147984/1‑139 (MQ=255)

                                                                                  cTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCg                                                                                                  >  1:120759/1‑89 (MQ=255)

                                                                                  cTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCg                                                                                                  <  2:120759/89‑1 (MQ=255)

                                                                                  cTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTctgctg                                                  >  1:281354/1‑137 (MQ=255)

                                                                                          aTCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGAt                                          <  1:97684/137‑1 (MQ=255)

                                                                                          aTCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGAt                                          <  2:6336/137‑1 (MQ=255)

                                                                                                aaCCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCata                                  <  2:308172/139‑1 (MQ=255)

                                                                                                      ggTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAgcg                                                              <  2:268774/105‑1 (MQ=255)

                                                                                                      ggTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAgcg                                                              >  1:268774/1‑105 (MQ=255)

                                                                                                          ccAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGa                        >  1:111817/1‑139 (MQ=255)

                                                                                                            aaCCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGAtt                      >  2:197544/1‑139 (MQ=255)

                                                                                                                       aCGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGc                                      >  2:176566/1‑112 (MQ=255)

                                                                                                                       aCGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGc                                      <  1:176566/112‑1 (MQ=255)

                                                                                                                             tGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGATTTTGAATTCGAAACCTAt     >  1:5248/1‑139 (MQ=255)

                                                                                                                                aGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGATTTTGAATTCGAAACCTATTAc  <  1:436344/139‑1 (MQ=255)

AAGGAACTGTTGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCTCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGATTTTGAATTCGAAACCTATTAC  >  NZ_CP009273/635317‑635583

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 34 ≤` `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

CAAGGAACTGTTGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCTCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGATTTTGAATTCGAAACCTATTACTCGCTCTCTTG  >  NZ_CP009273/635316‑635594

CAAGGAACTGTTGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAG                                                                                                                                  <  SRR3722119.29369/151‑1 (MQ=60)

         GTTGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCT                                                                                                                           <  SRR3722119.350875/149‑1 (MQ=60)

                    TCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGC                                                                                                              >  SRR3722119.243452/1‑151 (MQ=60)

                     CGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCGCGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGC                                                                                                              <  SRR3722119.325265/150‑1 (MQ=60)

                     CGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCG                                                                                                             <  SRR3722119.12787/151‑1 (MQ=60)

                              GTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGG                                                                                                    >  SRR3722119.333623/1‑151 (MQ=60)

                                           ACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATC                                                                                       <  SRR3722119.334429/151‑1 (MQ=60)

                                                    GAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAA                                                                                >  SRR3722119.6387/1‑149 (MQ=60)

                                                                        GCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCtgtctcttatacacatctccgagcccacgagactaaggc                                                          >  SRR3722119.121965/1‑112 (MQ=60)

                                                                        GCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGG                                                            >  SRR3722119.284260/1‑149 (MQ=60)

                                                                                          GATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTG                                          <  SRR3722119.98640/149‑1 (MQ=60)

                                                                                            atgtgtataagagacagAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGG                                      <  SRR3722119.178383/134‑1 (MQ=60)

                                                                                            TCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTctgtctcttatacacatctccg                                        >  SRR3722119.271553/1‑127 (MQ=60)

                                                                                                CAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGAT                                  >  SRR3722119.112913/1‑151 (MQ=60)

                                                                                                                   GGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGATTTTGAATTCGAAACCTATT               >  SRR3722119.5295/1‑151 (MQ=60)

                                                                                                                        ACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACtgtctcttatacacatctccgagcccacg           >  SRR3722119.41913/1‑121 (MQ=60)

                                                                                                                                CAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGATTTTGAATTCGAAACCTATTACTCGCTCTCTTG  <  SRR3722119.440707/151‑1 (MQ=60)

CAAGGAACTGTTGGCTGAAATCGCAGAACTGTCAGACAAAGTCACCTTTAAAGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCTCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCGCCATATTGACGGTGATTTTGAATTCGAAACCTATTACTCGCTCTCTTG  >  NZ_CP009273/635316‑635594

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`