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
A9 F1 I2 R1	760	52.7	2744488	90.2%	2475528	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,767,445	(C)_7→8	intergenic (+90/‑265)	rnlB → / → yfjP	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,767,438	1	.	C	93.1%	82.3 / ‑0.5	30	intergenic (+83/‑272)	rnlB/yfjP	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein
Reads supporting (aligned to +/- strand): ref base . (2/0); new base C (13/14); total (16/14)
Fisher's exact test for biased strand distribution p-value = 4.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGT  >  NC_000913/2767303‑2767565

ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cc                                                                                                                              >  2:687006/1‑139 (MQ=255)

  tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cccc                                                                                                                            <  1:687006/139‑1 (MQ=255)

               ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTc                                                                                                                <  1:166312/139‑1 (MQ=255)

                 gatgatGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTAGAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCt                                                                                                              <  1:1100717/139‑1 (MQ=255)

                             cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAaca                                                                                                  >  1:346678/1‑139 (MQ=255)

                               aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca                                                                                                                     <  1:219971/118‑1 (MQ=255)

                               aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca                                                                                                                     >  2:219971/1‑118 (MQ=255)

                                      tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc                                                                                         <  2:346678/139‑1 (MQ=255)

                                                      aCTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACt                                                                         <  1:598308/139‑1 (MQ=255)

                                                                    aCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAATC‑CCCCCCCTACAACGTCCTCCATAGAGAAACCGTTTTCCCCTTTGCACCCCCGACTCACTTTCCCCCCCt                                                           >  1:196113/1‑139 (MQ=255)

                                                                         ccAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCTCCCCCTTTaaa                                                      <  2:522744/139‑1 (MQ=255)

                                                                                  aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc                                                                                         <  2:149752/95‑1 (MQ=255)

                                                                                  aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc                                                                                         >  1:149752/1‑95 (MQ=255)

                                                                                     tCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca                                                                                                                     <  1:121025/64‑1 (MQ=255)

                                                                                     tCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca                                                                                                                     >  2:121025/1‑64 (MQ=255)

                                                                                      cGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑CACCCCCCTCACAACGTCCAGCATACGTAACACATTTTCCCATGTGGATCCACGACTAAATTTCACCCCCTTTAAAATACTCAATTATg                                         >  2:242181/1‑139 (MQ=255)

                                                                                       gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAac                                                                                                   >  1:606902/1‑80 (MQ=255)

                                                                                       gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAac                                                                                                   <  2:606902/80‑1 (MQ=255)

                                                                                       gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGt                                        <  2:40065/139‑1 (MQ=255)

                                                                                       gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGt                                        <  2:196113/139‑1 (MQ=255)

                                                                                                   tGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCTCTCTTTAAACTTCTCAATAATGTCACCAATTTTCt                            >  1:372932/1‑139 (MQ=255)

                                                                                                               gTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca                                                                                                                     >  2:1115293/1‑38 (MQ=255)

                                                                                                               gTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca                                                                                                                     <  1:1115293/38‑1 (MQ=255)

                                                                                                               gTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCCTAGGGAACACGTTTTCCCCTGTCCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATTTCACCAATTTTCTGGAAATCCTatg                >  1:801574/1‑139 (MQ=255)

                                                                                                               gTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAAGGAACACGTCTTCCCCTGTGCACCCACGACTAAATTTACCCCCCTTTAAACTTCACAATAATGTCACCAATTTTCGGGCATTCCTatg                >  1:1220994/1‑139 (MQ=255)

                                                                                                                tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGACCCCGCATTCCCATTTGCACCCCCGACTAAATTTACCACCCTTTAAACTTCTCAATAATGTCAACAATTTTCTGGAAATCTTatac               >  2:488129/1‑137 (MQ=255)

                                                                                                                tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCACAGGGAACACATTTTCCCCTGTGAACCCACGACTACACTTAACCCCCCTTAAAGTTTTCCATAATCTCTGCAATTTACTCGACATCCTatga               >  1:286433/1‑139 (MQ=255)

                                                                                                                tCCAATATGATCAAATAGCATTAA‑C‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTACACTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAGTGTCACCAATTTTCTGGAAATCCTatgat              >  1:881901/1‑139 (MQ=255)

                                                                                                                          tCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTccc     >  1:303233/1‑139 (MQ=255)

                                                                                                                          tCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAAAATCCCCCCCTTTAAACTTATCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTccc     >  1:1266513/1‑139 (MQ=255)

                                                                                                                           cAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg    <  2:811540/139‑1 (MQ=255)

                                                                                                                             aaTAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGt  <  2:286433/139‑1 (MQ=255)

CCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGT  >  NC_000913/2767303‑2767565

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A