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
A7 F28 I1 R1	252	48.5	1661298	98.8%	1641362	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,462,889	(C)_9→10	intergenic (+243/‑123)	fadL → / → yfdF	long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,462,880	1	.	C	90.9%	133.6 / 7.4	44	intergenic (+234/‑132)	fadL/yfdF	long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF
Reads supporting (aligned to +/- strand): ref base . (2/2); new base C (23/17); total (25/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

TTGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCATG  >  NC_000913/2462743‑2463014

ttGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cc                                                                                                                                      >  2:615066/1‑140 (MQ=255)

 tGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑ccc                                                                                                                                     <  2:422840/140‑1 (MQ=255)

  gCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑cccc                                                                                                                                    <  1:615066/140‑1 (MQ=255)

       cAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑ccccccccc                                                                                                                               <  1:712320/140‑1 (MQ=255)

                  cAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATtgt                                                                                                                     >  2:812014/1‑140 (MQ=255)

                  cAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATtgt                                                                                                                     >  1:590219/1‑140 (MQ=255)

                    gCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTgc                                                                                                                   >  1:227879/1‑140 (MQ=255)

                    gCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTgc                                                                                                                   >  2:173459/1‑140 (MQ=255)

                    gCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTgc                                                                                                                   >  1:196138/1‑140 (MQ=255)

                    gCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTgcg                                                                                                                  >  2:344756/1‑140 (MQ=255)

                             ttCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTgcg                                                                                                                  <  2:44873/132‑1 (MQ=255)

                             ttCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTgcg                                                                                                                  >  1:44873/1‑132 (MQ=255)

                               cAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACt                                                                                                        <  1:470466/140‑1 (MQ=255)

                                aaaTCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                                                       <  2:196138/140‑1 (MQ=255)

                                      aTAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTa                                                                                                 >  1:180429/1‑140 (MQ=255)

                                              tATCCACAGACAAACCTGAAGGGAAGGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAgg                                                                                         <  2:632634/140‑1 (MQ=255)

                                               aTCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                            >  2:604014/1‑136 (MQ=255)

                                               aTCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                            <  1:604014/136‑1 (MQ=255)

                                                tCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                       >  2:229262/1‑140 (MQ=255)

                                                tCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                       <  1:812014/140‑1 (MQ=255)

                                                tCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                       >  1:639716/1‑140 (MQ=255)

                                                tCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                       <  1:229262/140‑1 (MQ=255)

                                                      gACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCtaaa                                                                                  >  1:417319/1‑140 (MQ=255)

                                                        cAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCtaaataa                                                                               >  2:191141/1‑140 (MQ=255)

                                                           aCCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTaaataaat                                                                             >  1:253199/1‑140 (MQ=255)

                                                           aCCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATg                                                                            >  2:179945/1‑140 (MQ=255)

                                                            ccTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGa                                                                           >  1:89690/1‑140 (MQ=255)

                                                             cTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAg                                                                          <  1:546650/140‑1 (MQ=255)

                                                             cTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAg                                                                          <  2:59965/140‑1 (MQ=255)

                                                                aaGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGtt                                                                      <  1:344756/140‑1 (MQ=255)

                                                                     aaaGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGtttttt                                                                  <  2:639716/140‑1 (MQ=255)

                                                                        ggCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                                                <  2:253199/140‑1 (MQ=255)

                                                                             atTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCt                                                          >  1:139169/1‑140 (MQ=255)

                                                                               tttCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTAt                                                        >  2:519522/1‑140 (MQ=255)

                                                                                    ggCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAt                                                   <  1:519522/140‑1 (MQ=255)

                                                                                    ggCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAt                                                   >  1:461248/1‑140 (MQ=255)

                                                                                              tCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAatat                                         <  1:191141/140‑1 (MQ=255)

                                                                                                      ctcAAAGAGTTTACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGt                                 >  1:11145/1‑140 (MQ=255)

                                                                                                              gTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaatca                        >  2:638195/1‑140 (MQ=255)

                                                                                                               tttACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaatca                        >  2:522270/1‑140 (MQ=255)

                                                                                                                ttACTTTTCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaatcaa                       >  1:294779/1‑140 (MQ=255)

                                                                                                                      ttCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCaaaa                 <  1:109249/140‑1 (MQ=255)

                                                                                                                      ttCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCaaaa                 <  2:590219/140‑1 (MQ=255)

                                                                                                                      ttCTGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCaaaa                 <  2:563722/140‑1 (MQ=255)

                                                                                                                         tGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATgg              >  1:285479/1‑140 (MQ=255)

                                                                                                                         tGCATTTCCAGGATACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATAAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATgg              >  1:159068/1‑140 (MQ=255)

                                                                                                                                  aGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCa    <  1:638195/140‑1 (MQ=255)

                                                                                                                                     aTACTC‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCATg  <  2:227879/140‑1 (MQ=255)

TTGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑‑CCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATCATG  >  NC_000913/2462743‑2463014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A