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 I88 R1	217	30.5	1742422	95.9%	1670982	87.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	520,419	A→T	H568L (CAC→CTC)	rhsD →	rhs element protein RhsD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	520,419	0	A	T	100.0%	105.5 / NA	29	H568L (CAC→CTC)	rhsD	rhs element protein RhsD
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (15/14); total (15/14)

GCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCACCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCG  >  NZ_CP009273/520332‑520506

gCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCcg                                                                                      >  2:443485/1‑91 (MQ=255)

      ggCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGa                                                                                <  1:608152/91‑1 (MQ=255)

           ttGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCa                                                                           >  2:373589/1‑91 (MQ=255)

            tGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAt                                                                          <  2:367906/91‑1 (MQ=255)

            tGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAt                                                                          <  1:284024/91‑1 (MQ=255)

            tGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAt                                                                          <  1:541107/91‑1 (MQ=255)

               tGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAg                                                                       <  1:270025/91‑1 (MQ=255)

                    ttCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCttt                                                                  >  1:253711/1‑91 (MQ=255)

                      cACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTAc                                                                >  1:347745/1‑91 (MQ=255)

                             tGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCt                                                         <  2:856145/91‑1 (MQ=255)

                             tGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCt                                                         >  2:85375/1‑91 (MQ=255)

                              gCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTa                                                        >  2:411379/1‑91 (MQ=255)

                               cTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTAt                                                       >  2:43779/1‑91 (MQ=255)

                                tCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATg                                                      <  2:66849/91‑1 (MQ=255)

                                          aGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTgg                                            <  1:555639/91‑1 (MQ=255)

                                             cccGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCg                                         >  2:266197/1‑91 (MQ=255)

                                                gTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGtt                                      >  1:697196/1‑91 (MQ=255)

                                                 ttATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTa                                     <  1:85375/91‑1 (MQ=255)

                                                     gAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCt                                 <  1:111074/91‑1 (MQ=255)

                                                        tACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCgg                              <  2:719753/91‑1 (MQ=255)

                                                         aCGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGt                             >  1:191080/1‑91 (MQ=255)

                                                          cGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTg                            >  2:29205/1‑91 (MQ=255)

                                                          cGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTg                            >  1:737564/1‑91 (MQ=255)

                                                            aCCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAACAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGaa                          <  1:663686/91‑1 (MQ=255)

                                                               gCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGa                       >  1:86251/1‑91 (MQ=255)

                                                                         gATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGc             >  2:123292/1‑91 (MQ=255)

                                                                         gATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGc             <  2:697196/91‑1 (MQ=255)

                                                                              cggcggTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGa        >  1:868924/1‑91 (MQ=255)

                                                                                  ggTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcg    <  1:29205/91‑1 (MQ=255)

                                                                                    tcctccGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcgcg  <  1:798752/91‑1 (MQ=255)

                                                                                    tcctccGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcgcg  <  1:443485/91‑1 (MQ=255)

                                                                                    tcctccGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcgcg  <  2:799/91‑1 (MQ=255)

                                                                                    tcctccGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAAcgcg  <  1:116288/91‑1 (MQ=255)

GCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCACCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCG  >  NZ_CP009273/520332‑520506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TGACCTGGAGCCGCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCACCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAATAC  >  NZ_CP009273/520320‑520516

cagCCTGGAGCCGCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTC                                                                                                  <  SRR3722118.505119/98‑1 (MQ=60)

                  GGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGC                                                                                <  SRR3722118.621156/101‑1 (MQ=60)

                      GTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTT                                                                            >  SRR3722118.258880/1‑101 (MQ=60)

                        TGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTAC                                                                          <  SRR3722118.289860/101‑1 (MQ=60)

                        TGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTAC                                                                          >  SRR3722118.354953/1‑101 (MQ=60)

                        TGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTAC                                                                          <  SRR3722118.552586/101‑1 (MQ=60)

                           TGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGC                                                                       <  SRR3722118.275547/101‑1 (MQ=60)

                                                  TACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTT                                                >  SRR3722118.712408/1‑101 (MQ=60)

                                                      AGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACC                                            <  SRR3722118.567428/101‑1 (MQ=60)

                                                           CGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGT                                       >  SRR3722118.194863/1‑101 (MQ=60)

                                                            GTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTG                                      >  SRR3722118.753785/1‑101 (MQ=60)

                                                             TTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGA                                     <  SRR3722118.86958/101‑1 (MQ=60)

                                                                 GAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGA                                 <  SRR3722118.113129/101‑1 (MQ=60)

                                                                 GAATACGACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGA                                 >  SRR3722118.87847/1‑101 (MQ=60)

                                                                        ACCGCTTCGGCCAGATGACGGCGGTCCTCCGCGAGGAAGGCAACAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAG                          <  SRR3722118.678045/101‑1 (MQ=60)

                                                                                GGACAGATGACGGCGGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGA                  >  SRR3722118.888287/1‑101 (MQ=60)

                                                                                              GGTCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAAT    <  SRR3722118.29739/101‑1 (MQ=60)

                                                                                                TCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAATAC  <  SRR3722118.816304/101‑1 (MQ=60)

                                                                                                TCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAATAC  <  SRR3722118.452838/101‑1 (MQ=60)

                                                                                                TCCTCCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAATAC  <  SRR3722118.118445/101‑1 (MQ=60)

TGACCTGGAGCCGCTACGGGCAGTTGCTGGCGTTCACCGACTGCTCGGGCTACCAGACCCGTTATGAATACGACCGCTTCGGCCAGATGACGGCGGTCCACCGCGAGGAAGGCATCAGCCTTTACCGCCGCTATGACAACCGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAATAC  >  NZ_CP009273/520320‑520516

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`