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 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	453,695	G→A	A272T (GCG→ACG)	clpX →	ATP‑dependent protease ATP‑binding subunit ClpX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	453,695	0	G	A	96.4%	99.9 / NA	28	A272T (GCG→ACG)	clpX	ATP‑dependent protease ATP‑binding subunit ClpX
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (12/15); minor base C (1/0); total (13/15)
Fisher's exact test for biased strand distribution p-value = 4.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAA  >  NZ_CP009273/453571‑453829

tCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCg                                                                                                                          <  1:129379/139‑1 (MQ=255)

                 tGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGGTAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAaagcaag                                                                                                         >  1:294985/1‑139 (MQ=255)

                          aTACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGa                                                                                                <  2:285700/139‑1 (MQ=255)

                                 tAAGATCCTGTTTATTTGTGGCGGTGCGTTTTCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGGTCCGGCATTGGGTTTGGGACGACGGTAAAAACGAAGTCCGACAAAGCAAGGGAAGGCGAGctgctg                                                                                         >  1:279183/1‑139 (MQ=255)

                                        cTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGGTAAAGTGATTTTCCACCGTGTAGAAACCGGCTCCGGCATTGGGTTTGGCACGGCGGTAAAAGCGAAGACCGACAAAGAAAGCGAAGGCGGGCTGCTGGCGCAgg                                                                                  >  2:478830/1‑139 (MQ=255)

                                        cTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGGTAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGGTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAgg                                                                                  >  2:482057/1‑139 (MQ=255)

                                        cTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTTCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAgg                                                                                  >  2:5674/1‑139 (MQ=255)

                                        cTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAgg                                                                                  <  2:1493/139‑1 (MQ=255)

                                        cTGTTTATTTGTGGCGGTGCGTTTGCCGGGCTGGATAAAGTGATTTCCCCCCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAgg                                                                                  >  1:1493/1‑139 (MQ=255)

                                               tttGTGGCGGTGCGTTTGCCGGACTGGGTAAAGGGATTTTCCACCGTGTAGAAAACGGCTCCGGCATTGGTTTTGGGCCCACGGTAAAAGCGAAATCCGACAAAGCAAGCGAAAGCGAGCCGCCGGCGCAGGGTGAAcc                                                                           >  2:43818/1‑139 (MQ=255)

                                                  gtgGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCgg                                                                         <  1:372366/138‑1 (MQ=255)

                                                     gCGGTGCGTTTGCCGGGCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCgg                                                                         >  1:37826/1‑135 (MQ=255)

                                                           cGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGAt                                                               <  2:65090/139‑1 (MQ=255)

                                                                         gATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCtt                                                  <  1:450019/138‑1 (MQ=255)

                                                                              aGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCt                                            >  1:478042/1‑139 (MQ=255)

                                                                              aGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCt                                            <  2:478042/139‑1 (MQ=255)

                                                                                   tttCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTg                                           <  1:559579/135‑1 (MQ=255)

                                                                                   tttCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTg                                           >  2:559579/1‑135 (MQ=255)

                                                                                      cccACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTa                                     <  2:37826/138‑1 (MQ=255)

                                                                                             tgtAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGgacgt                             >  1:444298/1‑139 (MQ=255)

                                                                                               tAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCt                           >  2:276813/1‑139 (MQ=255)

                                                                                                     ccGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGt                     <  1:478830/139‑1 (MQ=255)

                                                                                                     ccGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGt                     <  2:458830/139‑1 (MQ=255)

                                                                                                         cTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTc                 >  2:34179/1‑139 (MQ=255)

                                                                                                              gCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAAc            <  1:546875/139‑1 (MQ=255)

                                                                                                              gCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAAc            <  1:43818/139‑1 (MQ=255)

                                                                                                               cATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACg           <  1:34179/139‑1 (MQ=255)

                                                                                                                         ggCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTtgaatgaa  <  1:482057/138‑1 (MQ=255)

TCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAA  >  NZ_CP009273/453571‑453829

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 18 ≤` `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

ATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGA  >  NZ_CP009273/453570‑453840

ATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGGCAA                                                                                                                          <  SRR3722139.130969/151‑1 (MQ=60)

       GCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGGTAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGC                                                                                                                   >  SRR3722139.298685/1‑151 (MQ=60)

                       GTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTTCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGGTCCGGCATTGGGTTTGGGACGACGGTAAAAACGAAGTCCGACAAAGCAAGGGAAGGCGAGCTGCTGG                                                                                                   >  SRR3722139.282700/1‑151 (MQ=60)

                              CCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGGCTGGATAAAGTGATTTCCCCCCGTGTAGAAACCGGCTCCGGCATTGGGTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGT                                                                                            >  SRR3722139.1506/1‑151 (MQ=60)

                                           GTTTATTTGTGGCGGTGCGTTTGCCGGGCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGGTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGA                                                                                   >  SRR3722139.38240/1‑147 (MQ=60)

                                                  TGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATC                                                                         <  SRR3722139.376835/150‑1 (MQ=60)

                                                      GCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTT                                                                    <  SRR3722139.467221/151‑1 (MQ=60)

                                                                    GGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTG                                                      >  SRR3722139.483623/1‑151 (MQ=60)

                                                                         GGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTT                                                  <  SRR3722139.455291/150‑1 (MQ=60)

                                                                               AGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGT                                           <  SRR3722139.565985/151‑1 (MQ=60)

                                                                                   ATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGACGTC                                       >  SRR3722139.449511/1‑151 (MQ=60)

                                                                                                     ACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGT                     <  SRR3722139.484414/151‑1 (MQ=60)

                                                                                                              GGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAAC            <  SRR3722139.44327/151‑1 (MQ=60)

                                                                                                              GGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAAC            <  SRR3722139.553163/151‑1 (MQ=60)

                                                                                                               GCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACT           <  SRR3722139.34551/151‑1 (MQ=60)

                                                                                                                    GGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCG      >  SRR3722139.314561/1‑151 (MQ=60)

                                                                                                                         TGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGA  <  SRR3722139.487668/150‑1 (MQ=60)

ATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACTGAGCGAAGA  >  NZ_CP009273/453570‑453840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`