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	782	316.7	10427156	97.0%	10114341	138.2

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%	108.6 / NA	29	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 (12/17); total (12/17)

AATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTT  >  NZ_CP025268/1219200‑1219465

aattaattAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCa                                                                                                                                <  2:1609011/140‑1 (MQ=255)

  ttaattaaAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCaaa                                                                                                                              <  2:3408651/140‑1 (MQ=255)

                    tatataAAATAAAATTTAAAGCAAGGGATCGCAATGGATGTTAAACAAAATTAGATTTTGTGAAAGCAATAAGTTATTGACTTCGTTTTACATTTGTATAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTaa                                                                                                            >  1:3111960/1‑140 (MQ=255)

                    tacataaaataaaATTTAAAGCAAGGAATCTTAATGGATGTTAAACAAAAGGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTAAACATCCTGTaa                                                                                                            >  2:2040906/4‑140 (MQ=255)

                      tataAAATAAAATTTACAGCAAGGAATCTCAAAGGATGGTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAAtt                                                                                                          <  1:1464970/140‑1 (MQ=255)

                      tataAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAAtt                                                                                                          <  1:1464599/140‑1 (MQ=255)

                           aataaaatTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAAc                                                                                                     >  1:357685/1‑140 (MQ=255)

                             taaaatTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACAt                                                                                                   <  2:3852075/140‑1 (MQ=255)

                                  tttAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCt                                                                                              <  2:357685/140‑1 (MQ=255)

                                                tctcAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTtgc                                                                                >  1:4584521/1‑139 (MQ=255)

                                                           gTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCt                                                                     <  2:754910/140‑1 (MQ=255)

                                                           gTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCt                                                                     <  1:3631089/140‑1 (MQ=255)

                                                            ttAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTa                                                                    <  2:5085776/140‑1 (MQ=255)

                                                              aaaCAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTaaa                                                                  >  2:1366343/1‑140 (MQ=255)

                                                                    aaTGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTAt                                                            >  2:1514196/1‑140 (MQ=255)

                                                                    aaTGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTAt                                                            >  2:1514273/1‑140 (MQ=255)

                                                                           ttttGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGcc                                                     <  1:549966/140‑1 (MQ=255)

                                                                                              tattGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGataata                                  <  1:385793/140‑1 (MQ=255)

                                                                                              tattGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGataata                                  <  1:385750/140‑1 (MQ=255)

                                                                                               attGACTTCGTTTTAGATTTGTTTAGCTATAATGTGATACATTCAAATGACTGAACATCCTGTAAGTAAAACATAGCCTTTATGCTACGTTGTGCCAATTTGCTAAACAGTATGGTCGCCTTTTTATATAACGAtaataa                                 <  1:3120208/140‑1 (MQ=255)

                                                                                                     ttCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAata                           >  1:1095070/1‑140 (MQ=255)

                                                                                                     ttCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAata                           >  2:3982295/1‑140 (MQ=255)

                                                                                                       cGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCa                                                                            <  1:579079/89‑1 (MQ=255)

                                                                                                       cGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCa                                                                            >  2:579079/1‑89 (MQ=255)

                                                                                                                tttGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGcatgaca                <  1:3982295/140‑1 (MQ=255)

                                                                                                                       aGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAAt         <  1:3272969/140‑1 (MQ=255)

                                                                                                                         cTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAat                            <  1:3060584/119‑1 (MQ=255)

                                                                                                                         cTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAat                            >  2:3060584/1‑119 (MQ=255)

                                                                                                                              aTGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGttt  >  2:3161114/1‑140 (MQ=255)

AATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTT  >  NZ_CP025268/1219200‑1219465

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

AAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAG  >  NZ_CP025268/1219209‑1219476

AAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGGATCGCAATGGATGTTAAACAAAATTAGATTTTGTGAAAGCAATAAGTTATTGACTTCGTTTTACATTTGTATAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAA                                                                                                                       >  SRR14920191.3120916/1‑151 (MQ=60)

       GGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAAC                                                                                                                >  SRR14920191.358723/1‑151 (MQ=60)

             TATAAAATAAAATTTACAGCAAGGAATCTCAAAGGATGGTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCC                                                                                                          <  SRR14920191.1468912/151‑1 (MQ=60)

             TATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCC                                                                                                          <  SRR14920191.1468541/151‑1 (MQ=60)

                            AAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGC                                                                                           >  SRR14920191.4598006/1‑151 (MQ=60)

                                           tgatcggtctcgtgggctcggagatgtgtataagagacagATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAAC                                                                            <  SRR14920191.580732/111‑1 (MQ=60)

                                                  cagaagacggcatacgagatactgatcggtctcgtgggctcggagatgtgtataagagacAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGG                                                                     <  SRR14920191.1421570/91‑1 (MQ=60)

                                                  cagaagacggcatacgagatactgatcggtctcgtgggctcggagatgtgtataagagacAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGG                                                                     <  SRR14920191.1421082/91‑1 (MQ=60)

                                                  GTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGG                                                                     <  SRR14920191.3641085/151‑1 (MQ=60)

                                                                  TTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAA                                                     <  SRR14920191.551516/151‑1 (MQ=60)

                                                                                 AAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATA                                      >  SRR14920191.1097986/1‑151 (MQ=60)

                                                                                     TATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAG                                  <  SRR14920191.386858/151‑1 (MQ=60)

                                                                                     TATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAG                                  <  SRR14920191.386901/151‑1 (MQ=60)

                                                                                      ATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTGATACATTCAAATGACTGAACATCCTGTAAGTAAAACATAGCCTTTATGCTACGTTGTGCCAATTTGCTAAACAGTATGGTCGCCTTTTTATATAACGATAATAATGAATATAAGC                                 <  SRR14920191.3129221/151‑1 (MQ=60)

                                                                                           taagagacaggatgTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGAC                            <  SRR14920191.3069202/137‑1 (MQ=60)

                                                                                                       TTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGG                <  SRR14920191.3993820/151‑1 (MQ=60)

                                                                                                              AGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAAT         <  SRR14920191.3282273/151‑1 (MQ=60)

                                                                                                                CTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTT       >  SRR14920191.4815696/1‑151 (MQ=60)

                                                                                                                  ATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAActgtctcttatacacatctccgagcccacgagaccgatc     >  SRR14920191.2637612/1‑112 (MQ=60)

                                                                                                                     ATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAG  >  SRR14920191.4692105/1‑151 (MQ=60)

AAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAG  >  NZ_CP025268/1219209‑1219476

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`