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 F50 I1 R1	775	316.5	10245680	97.2%	9958800	138.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP025268	1,219,333	G→A	intergenic (‑230/+27)	iraM ← / ← CXP41_RS24360	anti‑adapter protein IraM/protein YmgK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP025268	1,219,333	0	G	A	100.0%	78.4 / NA	22	intergenic (‑230/+27)	iraM/CXP41_RS24360	anti‑adapter protein IraM/protein YmgK
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (5/17); total (5/17)

ATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATG  >  NZ_CP025268/1219201‑1219436

attaattaAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCaa                                                                                                  <  1:2914261/140‑1 (MQ=255)

        aaaTGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGa                                                                                          <  1:3705056/140‑1 (MQ=255)

                 cTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGt                                                                                 <  2:1972499/140‑1 (MQ=255)

                   tatataAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTaa                                                                               >  2:1925335/1‑140 (MQ=255)

                                 tttAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCt                                                                 <  2:2915673/140‑1 (MQ=255)

                                           ggAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACt                                                       <  1:972817/140‑1 (MQ=255)

                                                  cAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGcc                                                >  1:1178213/1‑140 (MQ=255)

                                                     tGGATGTTAAACAAAATGAGATTGTGTGAAAGCAATAAATTATTGACTTCGTTTGAGATTTTTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTTCCAAt                                             >  2:4240503/1‑140 (MQ=255)

                                                          gTTAAACAACACGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTCTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGCACATCCTGTAATTAAAACATAGCCTTTATGCTACCTTGTGCCAAATTGCt                                        <  2:1264863/140‑1 (MQ=255)

                                                          gTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCt                                        <  1:253862/140‑1 (MQ=255)

                                                           ttAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTa                                       <  2:1178213/140‑1 (MQ=255)

                                                                   aaTGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTAt                               >  2:3176793/1‑140 (MQ=255)

                                                                      gagaTTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGt                            <  2:22199/140‑1 (MQ=255)

                                                                      gagaTTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGt                            <  2:477489/140‑1 (MQ=255)

                                                                        gaTTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTg                          <  2:3121098/140‑1 (MQ=255)

                                                                             tgtgAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTCAACATTCTGGTTGCCttt                     >  2:1841488/1‑140 (MQ=255)

                                                                                  aaGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTtata                <  2:2157226/140‑1 (MQ=255)

                                                                                   aGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTtatat               <  1:43909/140‑1 (MQ=255)

                                                                                     cAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATaa             <  2:999789/140‑1 (MQ=255)

                                                                                     cAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTCTTTATATaa             <  2:999732/140‑1 (MQ=255)

                                                                                             tattGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGataata     <  2:1507855/140‑1 (MQ=255)

                                                                                                tGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATg  <  1:2952352/140‑1 (MQ=255)

ATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATG  >  NZ_CP025268/1219201‑1219436

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAGTTATAT  >  NZ_CP025268/1219184‑1219482

CCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATAC                                                                                                                                                      <  SRR14920169.360599/151‑1 (MQ=60)

  CCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACAT                                                                                                                                                    <  SRR14920169.4541723/151‑1 (MQ=60)

                 ATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACA                                                                                                                                     <  SRR14920169.2921092/151‑1 (MQ=60)

                         AAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAA                                                                                                                             <  SRR14920169.3713683/151‑1 (MQ=60)

                                                        GCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCC                                                                                              >  SRR14920169.1180835/1‑151 (MQ=60)

                                                            GGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATT                                                                                          <  SRR14920169.975032/151‑1 (MQ=60)

                                                                           GTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGG                                                                           <  SRR14920169.254447/151‑1 (MQ=60)

                                                                                                    AGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAA                                                  <  SRR14920169.44064/151‑1 (MQ=60)

                                                                                                                 TGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCAT                                     <  SRR14920169.2959252/151‑1 (MQ=60)

                                                                                                                                              ATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAG        >  SRR14920169.2507371/1‑151 (MQ=60)

                                                                                                                                                    TACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAGTTATAT  <  SRR14920169.499343/151‑1 (MQ=60)

CCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAGTTATAT  >  NZ_CP025268/1219184‑1219482

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`