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	1,036,585	A→G	G171G (GGA→GGG)	appA →	bifunctional acid phosphatase/4‑phytase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,036,585	0	A	G	96.9%	112.4 / ‑2.8	32	coding (513/1299 nt)	appA	bifunctional acid phosphatase/4‑phytase
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (16/15); minor base . (1/0); total (17/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

TGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCA  >  NZ_CP009273/1036456‑1036717

tGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAAtt                                                                                                                             >  1:170707/1‑139 (MQ=255)

     gtgCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGa                                                                                                                        >  1:521766/1‑139 (MQ=255)

      tgCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGa                                                                                                                        <  2:151546/138‑1 (MQ=255)

      tgCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGAc                                                                                                                       >  1:307533/1‑139 (MQ=255)

        cAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACt                                                                                                                      <  1:192615/138‑1 (MQ=255)

                gTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCggg                                                                                                              >  1:347214/1‑138 (MQ=255)

                 tACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCa                                                                                                            >  1:163052/1‑139 (MQ=255)

                           ggCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAG‑‑GGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGc                                                                                                >  2:539147/1‑139 (MQ=255)

                            gCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACgg                                                                                                 >  1:79678/1‑139 (MQ=255)

                                aTACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGtt                                                                                             >  1:492066/1‑139 (MQ=255)

                                   cGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTc                                                                                           <  2:79678/138‑1 (MQ=255)

                                      ccAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTcgcg                                                                                        >  2:224487/1‑138 (MQ=255)

                                                tCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACgg                                                                             <  2:365914/139‑1 (MQ=255)

                                                    ttATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGaa                                                                                <  2:305889/132‑1 (MQ=255)

                                                    ttATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGaa                                                                                >  1:305889/1‑132 (MQ=255)

                                                            tCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAAtttt                                                                 >  1:408637/1‑139 (MQ=255)

                                                            tCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAAtttt                                                                 >  1:600222/1‑139 (MQ=255)

                                                             ccTCTAAAATCTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTc                                                                <  2:525620/139‑1 (MQ=255)

                                                                   aaaaCTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAAt                                                          <  1:224487/139‑1 (MQ=255)

                                                                          gCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACtt                                                   >  1:58770/1‑139 (MQ=255)

                                                                           cGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTtg                                                  <  2:163052/139‑1 (MQ=255)

                                                                                        gATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTg                                     <  1:513668/139‑1 (MQ=255)

                                                                                             cgcgAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGaaa                                >  1:147088/1‑139 (MQ=255)

                                                                                              gcgAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAAc                               <  2:147088/139‑1 (MQ=255)

                                                                                              gcgAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAAc                               <  2:492066/139‑1 (MQ=255)

                                                                                              gcgAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAAc                               <  1:109834/139‑1 (MQ=255)

                                                                                                       actgacGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGa                        >  2:51268/1‑137 (MQ=255)

                                                                                                       actgacGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGa                        >  2:62721/1‑137 (MQ=255)

                                                                                                        ctgacGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAg                     <  2:170707/139‑1 (MQ=255)

                                                                                                        ctgacGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAg                     <  2:347214/139‑1 (MQ=255)

                                                                                                                      agcagGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGc       <  2:58770/139‑1 (MQ=255)

                                                                                                                           ggcaggGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCa  >  1:57108/1‑139 (MQ=255)

TGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCA  >  NZ_CP009273/1036456‑1036717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `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

GGGCTGGCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACC  >  NZ_CP009273/1036445‑1036722

GGGCTGGCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTG                                                                                                                                 >  SRR3722135.173080/1‑151 (MQ=60)

     GGCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGAC                                                                                                                            >  SRR3722135.528679/1‑151 (MQ=60)

      GCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACT                                                                                                                           >  SRR3722135.311934/1‑151 (MQ=60)

                GTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGC                                                                                                                  >  SRR3722135.352126/1‑150 (MQ=60)

                 TGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCAT                                                                                                                >  SRR3722135.165292/1‑151 (MQ=60)

                  GCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCAT                                                                                                                <  SRR3722135.195345/150‑1 (MQ=60)

                            TACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGC                                                                                                     >  SRR3722135.80757/1‑151 (MQ=60)

                                TACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTT                                                                                                 >  SRR3722135.498660/1‑151 (MQ=60)

                                                    GTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCT                                                                             >  SRR3722135.310279/1‑151 (MQ=60)

                                                      gtttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTT                                                                            <  SRR3722135.206216/76‑1 (MQ=60)

                                                            CCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTC                                                                     >  SRR3722135.414294/1‑151 (MQ=60)

                                                            CCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTC                                                                     >  SRR3722135.608097/1‑151 (MQ=60)

                                                                          TCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTG                                                       >  SRR3722135.59555/1‑151 (MQ=60)

                                                                             AAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGC                                                    <  SRR3722135.227644/151‑1 (MQ=60)

                                                                                             CAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAAC                                    >  SRR3722135.149147/1‑151 (MQ=60)

                                                                                                  GGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGAC                               <  SRR3722135.520511/151‑1 (MQ=60)

                                                                                                        CGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGC                         <  SRR3722135.111323/151‑1 (MQ=60)

                                                                                                                           ATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCAT      >  SRR3722135.57875/1‑151 (MQ=60)

                                                                                                                                CAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACC  >  SRR3722135.608728/1‑150 (MQ=60)

GGGCTGGCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACC  >  NZ_CP009273/1036445‑1036722

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`