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 I177 R1	141	27.5	996908	97.7%	973979	124.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	557,194	A→G	Q681R (CAG→CGG)	sfmD →	fimbrial biogenesis usher protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	557,194	0	A	G	100.0%	94.2 / NA	27	Q681R (CAG→CGG)	sfmD	fimbrial biogenesis usher protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/10); total (17/10)

AGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGA  >  NZ_CP009273/557061‑557326

aGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGGATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGt                                                                                                                                 >  1:192173/1‑139 (MQ=255)

      cACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCg                                                                                                                           >  1:484598/1‑139 (MQ=255)

          tAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGgtgt                                                                                                                       >  2:270048/1‑139 (MQ=255)

                       tACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGa                                                                                                           >  2:84659/1‑138 (MQ=255)

                       tACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGa                                                                                                           >  2:71889/1‑138 (MQ=255)

                         ccTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGaaaa                                                                                                        <  2:484598/139‑1 (MQ=255)

                            cGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGGATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGGCGGGCATGAAAATgg                                                                                                     >  2:263947/1‑139 (MQ=255)

                             gAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATgg                                                                                                     >  2:18907/1‑138 (MQ=255)

                                         cacGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagc                                                                                        <  1:270048/139‑1 (MQ=255)

                                                 gcgcCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCtt                                                                                 >  2:323033/1‑138 (MQ=255)

                                                       cGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGa                                                                          >  2:483896/1‑139 (MQ=255)

                                                                 gCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcc                                                                                       >  1:378505/1‑116 (MQ=255)

                                                                 gCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcc                                                                                       <  2:378505/116‑1 (MQ=255)

                                                                                        ggggCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAgg                                         <  2:183224/139‑1 (MQ=255)

                                                                                         gggCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGc                                        <  1:323033/139‑1 (MQ=255)

                                                                                          ggCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGgcg                                             >  1:186394/1‑133 (MQ=255)

                                                                                          ggCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGgcg                                             <  2:186394/133‑1 (MQ=255)

                                                                                              ggTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTa                                                                               >  1:139017/1‑95 (MQ=255)

                                                                                              ggTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGgcgc                                            <  1:1585/130‑1 (MQ=255)

                                                                                              ggTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGgcgc                                            >  2:1585/1‑130 (MQ=255)

                                                                                              ggTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGAATGAAAATGGCATAACGCTGAGCCAGCCTTTa                                                                               <  2:139017/95‑1 (MQ=255)

                                                                                                         gACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcc                                                                                       >  2:1622/1‑76 (MQ=255)

                                                                                                         gACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGagcc                                                                                       <  1:1622/76‑1 (MQ=255)

                                                                                                                     cATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCa            >  1:201154/1‑139 (MQ=255)

                                                                                                                             tAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAAcc    >  2:112643/1‑139 (MQ=255)

                                                                                                                               aCTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGGGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGa  <  1:18907/139‑1 (MQ=255)

                                                                                                                               aCTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGa  >  1:280118/1‑139 (MQ=255)

AGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGA  >  NZ_CP009273/557061‑557326

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCGCGGCT  >  NZ_CP009273/557050‑557337

GCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGGATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTC                                                                                                                                           >  SRR3722131.194377/1‑151 (MQ=60)

      ACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGG                                                                                                                                     >  SRR3722131.489789/1‑151 (MQ=60)

                                                 GTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGTTGTCTGGCGGTGGGGCCGGGCATGAAAATGGCATAACGCTGAGCCtgtctctt                                                                                          >  SRR3722131.74067/1‑143 (MQ=60)

                                                   ACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGG                                                                                        <  SRR3722131.273191/151‑1 (MQ=60)

                                                    gcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacaGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGG                                                                                       <  SRR3722131.1637/99‑1 (MQ=60)

                                                                 ACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGctgtctcttatac                                                                          >  SRR3722131.382695/1‑138 (MQ=60)

                                                                                          GTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGG                                                 >  SRR3722131.188550/1‑151 (MQ=60)

                                                                                              GCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAActatctcttatacacatctccgagcccacgagac                                             >  SRR3722131.140575/1‑117 (MQ=60)

                                                                                                 GGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTAC                                            <  SRR3722131.1599/149‑1 (MQ=60)

                                                                                                   GGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCAT                                        <  SRR3722131.326688/151‑1 (MQ=60)

                                                                                                                     ACCGCGATCAACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCAT                      >  SRR3722131.203492/1‑151 (MQ=60)

                                                                                                                               ACATGACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGAC            >  SRR3722131.283356/1‑151 (MQ=60)

                                                                                                                                    ACGTTAACTGGCGGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCG       >  SRR3722131.138724/1‑151 (MQ=60)

                                                                                                                                         AACTGGCGGCTGTCTGTCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGGGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCGCGGCT  <  SRR3722131.19077/151‑1 (MQ=60)

GCCACAACCTGAGTTATCACGTAAGCCAGGGTGATACCTCGAATAATGGGTACACGGGCAGCGCCACGGCAAACTGGCAGGCCGCTTACGGTACGCTGGGGGGCGGGTATAACTACGACCGCGATCAACATGACGTTAACTGGCAGCTGTCTGGCGGTGTGGTCGGGCATGAAAATGGCATAACGCTGAGCCAGCCTTTAGGGGATACCAATGTTTTGATTAAAGCGCCTGGCGCAGGCGGTGTACGCATTGAAAATCAAACTGGCATTTTAACCGACTGGCGCGGCT  >  NZ_CP009273/557050‑557337

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`