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 F5 I97 R1	275	44.0	1733530	96.5%	1672856	122.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	857,539	T→C	E175G (GAA→GGA)	ybiW ←	glycyl radical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	857,539	0	T	C	100.0%	76.8 / NA	23	E175G (GAA→GGA)	ybiW	glycyl radical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/12); total (11/12)

TTCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTTCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACATGCCGTAGCAGCGA  >  NZ_CP009273/857409‑857661

ttCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCcagcag                                                                                                                     >  1:394810/1‑138 (MQ=255)

        ctgCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGa                                                                                                             >  2:31396/1‑138 (MQ=255)

        ctgCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGa                                                                                                             >  1:593698/1‑138 (MQ=255)

                           aaTCGCCTTCAGGAATTGCTCACCGTGTAAATCTTCCACCACCGTCAGGTTGATTCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTgcgc                                                                                          <  1:356639/138‑1 (MQ=255)

                            aTCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTgcgc                                                                                          >  1:315558/1‑137 (MQ=255)

                            aTCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTgcgc                                                                                          <  2:315558/137‑1 (MQ=255)

                                          ttGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCata                                                                          >  2:230376/1‑139 (MQ=255)

                                          ttGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCata                                                                          <  1:421867/139‑1 (MQ=255)

                                                      tAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGc                                                               <  1:99732/138‑1 (MQ=255)

                                                              ccAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGAt                                                      >  1:744149/1‑139 (MQ=255)

                                                                aGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTc                                                    <  2:593698/139‑1 (MQ=255)

                                                                      gTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCg                                              >  2:858346/1‑139 (MQ=255)

                                                                       tCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGc                                             >  1:643692/1‑139 (MQ=255)

                                                                            ttGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCcagca                                        <  1:586765/139‑1 (MQ=255)

                                                                                tGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGAcc                                    >  2:35101/1‑139 (MQ=255)

                                                                                        cgaCGTTCCGCTACTTCCTCGCTCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCt                            <  2:836661/139‑1 (MQ=255)

                                                                                        cgaCGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCt                            <  1:31396/139‑1 (MQ=255)

                                                                                        cgaCGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCt                            <  2:610072/139‑1 (MQ=255)

                                                                                        cgaCGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCt                            <  2:775130/139‑1 (MQ=255)

                                                                                                     cTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACa                <  2:643692/138‑1 (MQ=255)

                                                                                                     cTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACAt               >  2:523499/1‑139 (MQ=255)

                                                                                                               cAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACATGCCGTagcag     <  1:527164/139‑1 (MQ=255)

                                                                                                                  aCCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACATGCCGTAGCAGCGa  >  2:553439/1‑139 (MQ=255)

TTCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTTCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACATGCCGTAGCAGCGA  >  NZ_CP009273/857409‑857661

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 24 ≤` `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

GCAGCGAAACGTTCAATGTGTTCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTTCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACATGCCGTAGCAGCGATCCTGTACGGTCTGACCGCGCCACC  >  NZ_CP009273/857389‑857686

GCAGCGAAACGTTCAATGTGTTCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTC                                                                                                                                                     <  SRR3722120.341470/151‑1 (MQ=60)

GCAGCGAAACGTTCAATGTGTTCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTC                                                                                                                                                     >  SRR3722120.713650/1‑151 (MQ=60)

         CGTTCAATGTGTTCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGC                                                                                                                                             >  SRR3722120.400589/1‑150 (MQ=60)

                 GTGTTCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAA                                                                                                                                     >  SRR3722120.601983/1‑150 (MQ=60)

                                     GCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATC                                                                                                                >  SRR3722120.320121/1‑151 (MQ=60)

                                              CAATCGCCTTCAGGAATTGCTCACCGTGTAAATCTTCCACCACCGTCAGGTTGATTCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGG                                                                                                        <  SRR3722120.361808/150‑1 (MQ=60)

                                                             ATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGC                                                                                        <  SRR3722120.428041/151‑1 (MQ=60)

                                                                       GTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATT                                                                              >  SRR3722120.754223/1‑151 (MQ=60)

                                                                         GTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTC                                                                             <  SRR3722120.101061/150‑1 (MQ=60)

                                                                                TTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCC                                                                     >  SRR3722120.652549/1‑151 (MQ=60)

                                                                                               GTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGC                                                      <  SRR3722120.594940/151‑1 (MQ=60)

                                                                                                           GCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAAC                                          <  SRR3722120.31775/151‑1 (MQ=60)

                                                                                                                                  GCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACATGCCGTAGCAGCGATCCTGTAC                   <  SRR3722120.534663/151‑1 (MQ=60)

                                                                                                                                                   TTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACATGCCGTAGCAGCGATCCTGTACGGTCTGACCGCGCCACC  >  SRR3722120.398372/1‑151 (MQ=60)

GCAGCGAAACGTTCAATGTGTTCACTGACTGCCACCAGCACGATATCAATCGCTTTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTTCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTCCGGTCGCCAGCAGACCTTTTTGCTCATCGGTAAACATGCCGTAGCAGCGATCCTGTACGGTCTGACCGCGCCACC  >  NZ_CP009273/857389‑857686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`