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 I96 R1	227	23.3	882352	98.0%	864704	126.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	678,913	A→G	intergenic (‑64/+20)	hscC ← / ← rihA	molecular chaperone HscC/pyrimidine‑specific ribonucleoside hydrolase RihA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	678,913	0	A	G	100.0%	93.9 / NA	27	intergenic (‑64/+20)	hscC/rihA	molecular chaperone HscC/pyrimidine‑specific ribonucleoside hydrolase RihA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/12); total (15/12)

TCCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCG  >  NZ_CP009273/678783‑679048

tCCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTa                                                                                                                                    <  1:97179/136‑1 (MQ=255)

                      ggTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTaa                                                                                                            >  1:328281/1‑138 (MQ=255)

                                agaTCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGAc                                                                                                  >  2:70033/1‑138 (MQ=255)

                                  aTCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGAt                                                                                               >  2:71819/1‑139 (MQ=255)

                                     gATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAg                                                                                            >  2:295905/1‑139 (MQ=255)

                                                 gAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTaa                                                                                     <  1:146421/134‑1 (MQ=255)

                                                 gAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTaa                                                                                     >  2:146421/1‑134 (MQ=255)

                                                       tGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGc                                                                          >  2:424281/1‑139 (MQ=255)

                                                                cATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGAt                                                                 <  1:11723/139‑1 (MQ=255)

                                                                cATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGAt                                                                 <  1:295905/139‑1 (MQ=255)

                                                                   tGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCaa                                                              >  2:377814/1‑139 (MQ=255)

                                                                   tGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCaa                                                              >  1:316176/1‑139 (MQ=255)

                                                                       tttATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATc                                                          <  1:71819/139‑1 (MQ=255)

                                                                               ttGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTa                                                  >  2:373402/1‑139 (MQ=255)

                                                                                  aaagaaaAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACgg                                               <  1:207490/139‑1 (MQ=255)

                                                                                                       ttAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTg                          <  2:380120/139‑1 (MQ=255)

                                                                                                         aaGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGt                         <  1:167303/138‑1 (MQ=255)

                                                                                                                cccAGGTAACGCGTGGTGGTCTTAATCAATGTCGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaaca                                                                              <  1:155731/78‑1 (MQ=255)

                                                                                                                cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaaca                                                                              >  2:155731/1‑78 (MQ=255)

                                                                                                                cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGt                         <  1:418276/131‑1 (MQ=255)

                                                                                                                cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGt                         >  2:418276/1‑131 (MQ=255)

                                                                                                                cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGataa                  >  1:423374/1‑138 (MQ=255)

                                                                                                                cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGataa                  >  1:395155/1‑138 (MQ=255)

                                                                                                                         cgcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGt                         <  2:37752/122‑1 (MQ=255)

                                                                                                                         cgcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGt                         >  1:37752/1‑122 (MQ=255)

                                                                                                                           cgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATcaaca      <  1:70033/139‑1 (MQ=255)

                                                                                                                               gtgGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCg  >  1:40635/1‑139 (MQ=255)

TCCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCG  >  NZ_CP009273/678783‑679048

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

TGCGCGGCACCGTCTTTCCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCGTCATACCC  >  NZ_CP009273/678767‑679056

TGCGCGGCACCGTCTTTCCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCT                                                                                                                                              <  SRR3722119.408217/150‑1 (MQ=60)

               TTCCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGT                                                                                                                                 <  SRR3722119.98131/148‑1 (MQ=60)

                           ATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAA                                                                                                                   >  SRR3722119.331621/1‑150 (MQ=60)

                                                           AATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGC                                                                                  <  SRR3722119.147927/151‑1 (MQ=60)

                                                                  atacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGTCGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACG                                                                           <  SRR3722119.157324/100‑1 (MQ=60)

                                                                        GCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAAC                                                                     >  SRR3722119.319397/1‑151 (MQ=60)

                                                                               CCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACC                                                              <  SRR3722119.298925/151‑1 (MQ=60)

                                                                               CCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACC                                                              <  SRR3722119.11818/151‑1 (MQ=60)

                                                                                      ATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGG                                                       <  SRR3722119.72514/151‑1 (MQ=60)

                                                                                                 GAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGT                                            <  SRR3722119.209719/151‑1 (MQ=60)

                                                                                                                     GATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAAT                         >  SRR3722119.399095/1‑150 (MQ=60)

                                                                                                                     GATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAAT                         >  SRR3722119.427617/1‑150 (MQ=60)

                                                                                                                        TAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAAT                      <  SRR3722119.169028/150‑1 (MQ=60)

                                                                                                                        TAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAAT                      <  SRR3722119.422482/150‑1 (MQ=60)

                                                                                                                              CACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATctgtctc               >  SRR3722119.38086/1‑144 (MQ=60)

                                                                                                                                    GGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCGT         >  SRR3722119.40989/1‑151 (MQ=60)

                                                                                                                                          GCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCGTCATACC   <  SRR3722119.70717/151‑1 (MQ=60)

                                                                                                                                           CGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCGTCATACCC  <  SRR3722119.258059/151‑1 (MQ=60)

TGCGCGGCACCGTCTTTCCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCGTCATACCC  >  NZ_CP009273/678767‑679056

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`