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 R2	870	341.9	11209456	97.2%	10895591	138.9

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%	110.8 / NA	31	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 (7/24); total (7/24)

AATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACA  >  NZ_CP025268/1219200‑1219451

aattaattAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCa                                                                                                                  <  2:300111/140‑1 (MQ=255)

      ttaaAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGAc                                                                                                            <  1:4485522/140‑1 (MQ=255)

          aaTGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGaa                                                                                                        <  2:4494874/140‑1 (MQ=255)

                ggCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCt                                                                                                  <  1:3456523/140‑1 (MQ=255)

                ggCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCt                                                                                                  <  1:3456541/140‑1 (MQ=255)

                ggCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCt                                                                                                  <  2:393572/140‑1 (MQ=255)

                ggCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCt                                                                                                  <  2:1848221/140‑1 (MQ=255)

                  cTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGt                                                                                                <  2:4954505/140‑1 (MQ=255)

                    tatataAAATAAAATTTAAAGCATGGTATCACAATGGATGTTAAACAAAATCAGATTTTGTGAAAGCAATAATTTATTGACTTCGTTTTACATGTGTGTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTaa                                                                                              >  1:3350389/1‑140 (MQ=255)

                           aataaaatTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAAc                                                                                       >  1:3512608/1‑140 (MQ=255)

                             taaaatTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACAt                                                                                     <  2:3330272/140‑1 (MQ=255)

                                aatTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGc                                                                                  >  2:1282822/1‑140 (MQ=255)

                                  tttAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCt                                                                                <  2:5319869/140‑1 (MQ=255)

                                  tttAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCt                                                                                <  2:4945643/140‑1 (MQ=255)

                                     aaaGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTa                                                                             >  1:1564579/1‑140 (MQ=255)

                                                    aaTGGATGTTAAACAAAATGAGATTTTGTGAACGCAATAAATTATTGACTTCGTTTTAGAGTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTGTATGCTACTTTGTGCCa                                                              <  2:2066636/140‑1 (MQ=255)

                                                       ggATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAAtt                                                           >  1:3766094/1‑140 (MQ=255)

                                                          tGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACAGTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGc                                                        <  2:5431394/140‑1 (MQ=255)

                                                           gTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCa                                                                                                                  >  1:695512/1‑81 (MQ=255)

                                                           gTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCa                                                                                                                  <  2:695512/81‑1 (MQ=255)

                                                                    aaTGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATg                                                                           >  1:849111/1‑111 (MQ=255)

                                                                    aaTGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATg                                                                           <  2:849111/111‑1 (MQ=255)

                                                                       tagaTTTTGTGAAAGCAATCAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGt                                           <  2:2659067/139‑1 (MQ=255)

                                                                         gaTTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTg                                         <  1:308727/140‑1 (MQ=255)

                                                                         gaTTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTg                                         <  1:303236/140‑1 (MQ=255)

                                                                                          aaaTTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGat                        <  1:1160857/140‑1 (MQ=255)

                                                                                              tattGACTTCGTTATAGATTTGTTTAACTATAATGTTATAGATTAAAAAGACTGAAAATACTGTAATTAATACCTAGCCTTTATGCTACTTCGTGACAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGataata                    <  2:12923/140‑1 (MQ=255)

                                                                                                    cTTCGTTTTAGATTTGTTTAGCTATAATGTTATACCTTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTGTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAat              <  2:3198851/140‑1 (MQ=255)

                                                                                                       cGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAAtata           <  1:2089575/140‑1 (MQ=255)

                                                                                                                tttGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGcatgaca  <  1:4205552/140‑1 (MQ=255)

                                                                                                                tttGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGcatgaca  <  1:4205332/140‑1 (MQ=255)

AATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACA  >  NZ_CP025268/1219200‑1219451

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

CCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAGTTAT  >  NZ_CP025268/1219186‑1219480

CCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACAT                                                                                                                                                  <  SRR14920167.3739966/151‑1 (MQ=60)

CCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACAT                                                                                                                                                  <  SRR14920167.3739643/151‑1 (MQ=60)

                    TTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTG                                                                                                                              <  SRR14920167.4495588/151‑1 (MQ=60)

                       AAATGATGGCTTATATAAAATAAAATTTAAAGCATGGTATCACAATGGATGTTAAACAAAATCAGATTTTGTGAAAGCAATAATTTATTGACTTCGTTTTACATGTGTGTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAA                                                                                                                           >  SRR14920167.3357760/1‑151 (MQ=60)

                              GGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAAC                                                                                                                    >  SRR14920167.3520329/1‑151 (MQ=60)

                              GGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAAC                                                                                                                    <  SRR14920167.3464192/151‑1 (MQ=60)

                              GGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAAC                                                                                                                    <  SRR14920167.3464174/151‑1 (MQ=60)

                                        AAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTA                                                                                                          >  SRR14920167.1567764/1‑151 (MQ=60)

                                                      cctaacggagacctttttttcaagcagaagacggcatacgagatgcagcgtagtctcgtgggctcggagatgtgtataagagacagATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCC                                                                                            <  SRR14920167.2139815/65‑1 (MQ=60)

                                                      atacacacgttcttttttttcaagcagaagacggcatacgagatgcagcgtagtctcgtgggctcggagatgtgtataagagacagATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCC                                                                                            <  SRR14920167.2139828/65‑1 (MQ=60)

                                                          GGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATT                                                                                        >  SRR14920167.3774218/1‑151 (MQ=60)

                                                              TCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACctgtctcttatacacatctccgagcccacgagactacgctgcatctcg                                                                                    >  SRR14920167.697064/1‑103 (MQ=60)

                                                                       ATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCtgtctcttatacacatc                                                                           >  SRR14920167.850956/1‑134 (MQ=60)

                                                                                       GATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATAT                                                           <  SRR14920167.303973/151‑1 (MQ=60)

                                                                                       GATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATAT                                                           <  SRR14920167.309476/151‑1 (MQ=60)

                                                                                                  gtagtctcgtgggctcggagatgtgtataagagacAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAA                                                <  SRR14920167.2806123/116‑1 (MQ=60)

                                                                                                        AAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATA                                          <  SRR14920167.1163213/151‑1 (MQ=60)

                                                                                                                     CGTTTTAGATTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATG                             <  SRR14920167.2093961/151‑1 (MQ=60)

                                                                                                                              TTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGG                    <  SRR14920167.4214683/151‑1 (MQ=60)

                                                                                                                              TTTGTTTAGCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGG                    <  SRR14920167.4214903/151‑1 (MQ=60)

                                                                                                                                      GCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATT            >  SRR14920167.455347/1‑151 (MQ=60)

                                                                                                                                      GCTATAATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATT            >  SRR14920167.455524/1‑151 (MQ=60)

                                                                                                                                            ATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATTCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAG      >  SRR14920167.2296342/1‑151 (MQ=60)

                                                                                                                                            ATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAG      >  SRR14920167.2697843/1‑151 (MQ=60)

                                                                                                                                            ATGTTATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAG      >  SRR14920167.3146181/1‑151 (MQ=60)

                                                                                                                                                TATACATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATctgtctcttatacacatctccgagcccacgagactacgctg  >  SRR14920167.2992349/1‑110 (MQ=60)

CCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTTTTAGATTTGTTTAGCTATAATGTTATGCATTCAAATGACTGAACATCCTGTAATTAAAACATAGCCTTTATGCTACTTTGTGCCAATTTGCTAAACATTATGGTTGCCTTTTTATATAACGATAATAATGAATATAAGCATGACATGAGAATAAGGTTTCAATTTTTGAGTTAT  >  NZ_CP025268/1219186‑1219480

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`