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	780,389	A→G	intergenic (‑110/+4)	zitB ← / ← ybgS	CDF family zinc transporter ZitB/YbgS‑like family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	780,389	0	A	G	100.0%	118.7 / NA	33	intergenic (‑110/+4)	zitB/ybgS	CDF family zinc transporter ZitB/YbgS‑like family protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/16); total (17/16)

GTGTGTGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCAGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGCACA  >  NZ_CP009273/780257‑780493

gtgtgtGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTa                                                                                                    <  2:361577/139‑1 (MQ=255)

gtgtgtGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTa                                                                                                    >  1:250039/1‑139 (MQ=255)

 tgtgtgAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTAc                                                                                                   >  2:400767/1‑139 (MQ=255)

   tgtgagtgtgagTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACt                                                                                                  <  1:619645/138‑1 (MQ=255)

       agtgtgagtgCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGt                                                                                              <  1:193840/138‑1 (MQ=255)

             agtgCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCg                                                                                       >  1:183694/1‑139 (MQ=255)

             agtgCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCg                                                                                       >  1:515659/1‑139 (MQ=255)

             agtgCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCg                                                                                       <  1:400767/139‑1 (MQ=255)

              gtgCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGt                                                                                      <  2:179228/139‑1 (MQ=255)

                 cgcCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCgg                                                                                   >  1:321727/1‑139 (MQ=255)

                  gcCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGt                                                                                  >  2:588850/1‑139 (MQ=255)

                            gTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATc                                                                         >  2:535439/1‑138 (MQ=255)

                                tCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGAcat                                                                    <  1:139358/139‑1 (MQ=255)

                                                aCTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCAt                                                     >  1:429940/1‑138 (MQ=255)

                                                 cTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCa                                                   >  1:51285/1‑139 (MQ=255)

                                                    aaCTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCAcc                                                 <  2:566493/138‑1 (MQ=255)

                                                           tGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTa                                         <  2:51285/139‑1 (MQ=255)

                                                                tcatACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCttt                                    <  2:429940/139‑1 (MQ=255)

                                                                 catACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCtttt                                   >  2:405654/1‑139 (MQ=255)

                                                                               aaGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGa                     <  2:515659/139‑1 (MQ=255)

                                                                                  tGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAg                  >  2:383457/1‑139 (MQ=255)

                                                                                  tGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAg                  >  1:71231/1‑139 (MQ=255)

                                                                                  tGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAg                  >  2:2200/1‑139 (MQ=255)

                                                                                  tGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAg                  >  1:606299/1‑139 (MQ=255)

                                                                                    aaaaaTTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTa                                                                                                    <  2:385992/55‑1 (MQ=255)

                                                                                    aaaaaTTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTa                                                                                                    >  1:385992/1‑55 (MQ=255)

                                                                                      aaaTTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGAc              <  1:535439/139‑1 (MQ=255)

                                                                                      aaaTTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGAc              <  1:383457/139‑1 (MQ=255)

                                                                                                  agagaCTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGcaca  <  1:2200/139‑1 (MQ=255)

                                                                                                        tCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGAc              <  2:30799/121‑1 (MQ=255)

                                                                                                        tCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGAc              >  1:30799/1‑121 (MQ=255)

                                                                                                                                 tGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTg                                           <  1:91252/67‑1 (MQ=255)

                                                                                                                                 tGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTg                                           >  2:91252/1‑67 (MQ=255)

GTGTGTGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCAGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGCACA  >  NZ_CP009273/780257‑780493

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `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

GGTGTGAGGACGTGTGTGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCAGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGCACATGGTGTTCTTG  >  NZ_CP009273/780246‑780504

GGTGTGAGGACGTGTGTGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTAC                                                                                                              >  SRR3722135.253570/1‑151 (MQ=60)

             GTGTGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGT                                                                                                 >  SRR3722135.186262/1‑151 (MQ=60)

             GTGTGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGT                                                                                                 >  SRR3722135.522521/1‑151 (MQ=60)

             GTGTGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCG                                                                                                  <  SRR3722135.627760/150‑1 (MQ=60)

                 GAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGT                                                                                             >  SRR3722135.326330/1‑151 (MQ=60)

                 GAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGG                                                                                              <  SRR3722135.196583/150‑1 (MQ=60)

                       GAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGT                                                                                       <  SRR3722135.406319/151‑1 (MQ=60)

                                          ATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATG                                                                    <  SRR3722135.141278/151‑1 (MQ=60)

                                                TAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATC                                                               >  SRR3722135.435799/1‑150 (MQ=60)

                                                 AATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCAC                                                             >  SRR3722135.51978/1‑151 (MQ=60)

                                                          CACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCtgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgt                                                    >  SRR3722135.616624/1‑96 (MQ=60)

                                                                   cagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTAT                                           <  SRR3722135.92475/89‑1 (MQ=60)

                                                                                  GCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGC                            >  SRR3722135.614226/1‑151 (MQ=60)

                                                                                  GCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGC                            >  SRR3722135.72190/1‑151 (MQ=60)

                                                                                    TTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCtgtctcttatacacatctccgagcccacgagaccgtactagatatcgtatgccgtcttctgcttgaaaaaaa                           >  SRR3722135.391369/1‑78 (MQ=60)

                                                                                                AAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGCAC              <  SRR3722135.388802/151‑1 (MQ=60)

                                                                                                AAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGCAC              <  SRR3722135.542523/151‑1 (MQ=60)

                                                                                                        AAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGCACctgtctct      >  SRR3722135.31217/1‑143 (MQ=60)

                                                                                                            GAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCGGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGCACATGGTGTTCTTG  <  SRR3722135.2235/151‑1 (MQ=60)

GGTGTGAGGACGTGTGTGAGTGTGAGTGCGCCATGACGAGTCATCCCTTAATTATTCTCACTTAACTTTATGACATCATACTGCTTTTAGAAGTGAAAAATTAAAAGGGAGAGACTCCGCTCTCCCATTATTGGCTATTTTGCAGGGTTACTGCGTGGTACCGTCGGTTTTGGTATCGACATCATTATTGATGCCATCACCGGTTTGTACCTTTTTATTGATATCCGGACAGCGACCATCTTTGCACATGGTGTTCTTG  >  NZ_CP009273/780246‑780504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`