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 I179 R1	182	40.3	1547118	96.8%	1497610	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	659,797	A→C	S284A (TCG→GCG)	rlpA ←	endolytic peptidoglycan transglycosylase RlpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	659,797	0	A	C	100.0%	96.1 / NA	27	S284A (TCG→GCG)	rlpA	endolytic peptidoglycan transglycosylase RlpA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (15/12); total (15/12)

CCGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGAGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTG  >  NZ_CP009273/659668‑659919

ccGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTg                                                                                                                   <  2:462612/139‑1 (MQ=255)

    gcCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGgt                                                                                                               >  1:193413/1‑139 (MQ=255)

                  cgcgACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAgg                                                                                                 >  2:73882/1‑139 (MQ=255)

                  cgcgACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAgg                                                                                                 >  2:391025/1‑139 (MQ=255)

                          gggACGCCGAACTTCTGTCCCAGTCGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTg                                                                                         >  2:469211/1‑139 (MQ=255)

                                 cGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGt                                                                                  >  2:564272/1‑139 (MQ=255)

                                        cTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGa                                                                            <  1:564272/138‑1 (MQ=255)

                                        cTGTCCCAGTCGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGa                                                                            <  1:469211/138‑1 (MQ=255)

                                           tCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACgg                                                                         <  2:476484/138‑1 (MQ=255)

                                           tCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACgg                                                                         <  2:366089/138‑1 (MQ=255)

                                                                 tGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAgg                                                                                                 >  2:85347/1‑92 (MQ=255)

                                                                 tGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAgg                                                                                                 <  1:85347/92‑1 (MQ=255)

                                                                 tGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGgcg                                                  >  2:268405/1‑139 (MQ=255)

                                                                 tGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGgcg                                                  >  1:763611/1‑139 (MQ=255)

                                                                     cACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAgg                                              >  2:361738/1‑139 (MQ=255)

                                                                          gCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCg                                         >  1:413999/1‑139 (MQ=255)

                                                                               aTCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCg                                    <  1:268405/139‑1 (MQ=255)

                                                                                  gCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGTCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCTCAGGCGTCGGTTCGCTg                                 <  1:79161/139‑1 (MQ=255)

                                                                                    ttACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGcc                               >  1:67263/1‑139 (MQ=255)

                                                                                         gCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGcc                               <  1:565479/134‑1 (MQ=255)

                                                                                         gCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGcc                               >  2:565479/1‑134 (MQ=255)

                                                                                         gCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCa                          <  1:616640/139‑1 (MQ=255)

                                                                                                   gCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCa                  <  2:350236/137‑1 (MQ=255)

                                                                                                         tAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCt            >  1:693969/1‑137 (MQ=255)

                                                                                                                 ccGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGa                                                                            <  1:757684/65‑1 (MQ=255)

                                                                                                                 ccGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGa                                                                            >  2:757684/1‑65 (MQ=255)

                                                                                                                 ccGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTg  >  2:585272/1‑139 (MQ=255)

CCGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGAGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTG  >  NZ_CP009273/659668‑659919

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

GGATCCGCCAGACCGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGAGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTA  >  NZ_CP009273/659656‑659910

GGATCCGCCAGACCGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTT                                                                                                           <  SRR3722133.525894/150‑1 (MQ=60)

     CGCCAGACCGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTG                                                                                                     >  SRR3722133.195982/1‑151 (MQ=60)

                             acggtctcgtgggctcggagatgtgtataagagacagGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAG                                                                             <  SRR3722133.86457/114‑1 (MQ=60)

                                                  agcagaagacggcatacgagatctagtacggtctcgtgggctcagagatgtgtataagagacagCCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAA                                                        <  SRR3722133.767488/87‑1 (MQ=60)

                                                   TCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAA                                                        <  SRR3722133.571768/150‑1 (MQ=60)

                                                   TCTGTCCCAGTCGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAA                                                        <  SRR3722133.475588/150‑1 (MQ=60)

                                                                  GTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGC                                        >  SRR3722133.773489/1‑151 (MQ=60)

                                                                           GTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGG                               >  SRR3722133.419721/1‑151 (MQ=60)

                                                                                     AGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCT                     >  SRR3722133.68110/1‑151 (MQ=60)

                                                                                          GATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAG                <  SRR3722133.272056/151‑1 (MQ=60)

                                                                                             CGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGTCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCTCAGGCGTCGGTTCGCTGCCTACCAGTAC             <  SRR3722133.80161/151‑1 (MQ=60)

                                                                                                 TACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACAC           <  SRR3722133.572984/149‑1 (MQ=60)

                                                                                                    GGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGC      <  SRR3722133.624752/151‑1 (MQ=60)

                                                                                                          GACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTA  >  SRR3722133.702974/1‑149 (MQ=60)

GGATCCGCCAGACCGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGAGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTA  >  NZ_CP009273/659656‑659910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`